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Self Assembly in Soft Matter

Alexandros Chremos

Doctor of Philosophy
University of Edinburgh
2008
Declaration

I declare that this thesis was composed by myself and that the work contained therein
is my own, except where explicitly stated otherwise in the text.

(Alexandros Chremos)

i
To my parents

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Abstract

The term “soft matter” applies to a variety of physical systems, such as liquids,
colloids, polymers, foams, gels, and granular materials. The most fascinating aspect
of soft matter lies in the fact that they are not atomic or molecular in nature. They
are instead macromolecular aggregates, whose spatial extent lies in the domain 1 nm
to 1 µm.
Some of the most important examples of soft matter are polymers, which exhibit
intriguing and useful physical properties. In this work, the adsorption and self assem-
bly of linear and star polymers on smooth surfaces are studied using coarse-grained,
bead-spring molecular models and Langevin dynamics computer simulations. The
aim is to gain insight on atomic-force microscopy images of polymer films on mica
surfaces, adsorbed from dilute solution following a good solvent-to-bad solvent
quenching procedure. In the case of linear polymers, under certain experimental
conditions, a bimodal cluster distribution is observed. It is demonstrated that this
type of distribution can be reproduced in the simulations, and rationalized on the
basis of the polymer structures prior to the quench. In addition to providing insight
on experimental observations, the simulation results support a number of predicted
scaling laws such as the decay of the monomer density as a function of distance from
the surface, and the scaling of the film height with the strength of the polymer-surface
interactions.
Star polymers represent a special class of polymers, in which one end of each
linear chain is tethered to a small central core to form a single particle. The discovery
of these molecules led to the synthesis of a wide range of new materials. Their
structures are effectively considered as intermediate between those of colloids and
linear polymers. We explore the behaviour of the star polymers (which are like
“soft colloids”) in the proximity of a surface, using Langevin dynamics simulations.
A number of different measurements such as the height, radius of gyration, and
asphericity of adsorbed stars with different number of arms, are shown to provide
valuable insights on experimental findings.
The simplest soft matter systems consist of spherical, rigid colloidal particles.

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ABSTRACT iv

Examples of such particles are chemically synthesized polystyrene or silica particles.


We investigated the neighbour distribution in a two-dimensional polydisperse hard-
disk fluid, corresponding physically to a colloidal monolayer. The disk diameter
distribution was defined by a power-law with the aim of realizing a scale-free near-
neighbour network. Scale-free (power-law) behaviour is found in many important
networks, for example, in transportation systems, biochemical reactions, scientific
and movie-actor collaborations, and sexual contacts. We have provided the first
example of a scale-free network in a model condensed-matter system.
Finally, we use genetic algorithms, a method for efficiently searching for minima
on energy landscapes, to investigate the ordered equilibrium structures formed
by binary mixtures of anisotropic dipolar particles confined on a plane, under the
presence of an external magnetic field. The anisotropy of the interparticle forces is
controlled by tilting the external magnetic field with respect to the plane. Initially, as
the field is tilted the structures are only slightly perturbed, but once the anisotropy
exceeds a critical value, completely new structures emerge.
Acknowledgments

I would like to thank my advisor Dr. Philip J. Camp for teaching me how to do
research. His confidence in my work was very supportive and it encouraged me
greatly. I always had the freedom to follow my own ideas, for which I am very grateful.
I would like to thank my (informal) advisor Dr. Vasileios Koutsos, who initiated
the polymer projects. The fact that I could spend time in a different department gave
me the opportunity to see things from a different perspective. Additionally, I would
like to thank Dr. Emmanouil Glynos for the endless discussions about polymers and
other subjects.
I would like to thank Prof. Christos N. Likos for giving me the chance to learn
and work with genetic algorithms during a three month visit to the Department of
Theoretical Physics, University of Düsseldorf, whose support via SFB and hospitality
are gratefully acknowledged. In addition, I am grateful to Julia Fornleitner for valuable
discussions about genetic algorithms.
Former and current colleagues from our group, namely Peter Duncan, Leonardo
Lenoci and Georg Gunzemuller, never ceased to amazed me with their actions in our
group meetings especially those abroad which were carefully planned and organised
by our advisor, Dr. Philip J. Camp.
Finally but not least I thank for the financial support of the EPSRC and the School
of Chemistry of the University of Edinburgh.

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Contents

Declaration i

Abstract iii

Acknowledgments v

1 Introduction 1
1.1 Polymers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.2 Scale-free neighbour networks in polydisperse 2D fluids . . . . . . . . . 5
1.3 Colloidal monolayers with dipolar interactions . . . . . . . . . . . . . . 6
1.4 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

2 General Considerations 8
2.1 Statistical physics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
2.1.1 Ensembles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
2.1.2 Time averages and ensemble averages . . . . . . . . . . . . . . . 10
2.2 Simulation Techniques . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
2.2.1 Interaction potentials . . . . . . . . . . . . . . . . . . . . . . . . . 11
2.2.2 Reduced Units . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
2.2.3 Periodic Boundary Conditions . . . . . . . . . . . . . . . . . . . . 13
2.2.4 Monte Carlo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
2.2.5 Molecular dynamics . . . . . . . . . . . . . . . . . . . . . . . . . . 15
2.2.6 Brownian dynamics . . . . . . . . . . . . . . . . . . . . . . . . . . 17
2.3 Polymers and Scaling Theory . . . . . . . . . . . . . . . . . . . . . . . . . 18
2.3.1 Definition and structure . . . . . . . . . . . . . . . . . . . . . . . . 18
2.3.2 Polymer conformations . . . . . . . . . . . . . . . . . . . . . . . . 19
2.3.3 Solvent effects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
2.3.4 Scaling concepts of polymers . . . . . . . . . . . . . . . . . . . . . 23
2.4 Fractals and self-similarity . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
2.4.1 Fractal dimension and Koch curve . . . . . . . . . . . . . . . . . . 25
2.4.2 Fractal universe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

3 Adsorption and self-assembly of linear polymers on surfaces 29


3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
3.2 Simulation model and methods . . . . . . . . . . . . . . . . . . . . . . . 32
3.3 Results & discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
3.3.1 Isolated polymer . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
3.3.2 Many polymers – good solvent . . . . . . . . . . . . . . . . . . . . 39

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CONTENTS vii

3.3.3 Many polymers – bad solvent . . . . . . . . . . . . . . . . . . . . . 44


3.4 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47

4 Adsorption and self-assembly of star polymers on surfaces 49


4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
4.2 Simulation Model & Methods . . . . . . . . . . . . . . . . . . . . . . . . . 52
4.2.1 Simulation Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
4.3 Results & Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
4.3.1 Isolated star – Athermal solvent . . . . . . . . . . . . . . . . . . . 53
4.3.2 Isolated star - Solvent Effects . . . . . . . . . . . . . . . . . . . . . 62
4.3.3 Many adsorbed stars - Athermal solvent . . . . . . . . . . . . . . 65
4.3.4 Many adsorbed stars - Bad Solvent . . . . . . . . . . . . . . . . . . 69
4.4 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70

5 Neighbor network in a polydisperse hard disk fluid 72


5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
5.2 Model and methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
5.2.1 Monte Carlo simulations . . . . . . . . . . . . . . . . . . . . . . . 76
5.2.2 Scaled particle theory . . . . . . . . . . . . . . . . . . . . . . . . . 78
5.2.3 Degree distribution from maximum-entropy theory . . . . . . . 79
5.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
5.3.1 Equation of state . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
5.3.2 Radical tessellation and degree distribution . . . . . . . . . . . . 81
5.3.3 Assortativity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
5.4 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88

6 Crystal structures of 2D binary mixtures of dipolar colloids in tilted fields 90


6.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
6.2 Simulation Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
6.2.1 Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
6.2.2 Interactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
6.2.3 Genetic Algorithms . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
6.3 Results & Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
6.3.1 C ≥ 1/2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
6.3.2 C < 1/2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
6.3.3 Density effects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
6.3.4 Diameter ratio effects . . . . . . . . . . . . . . . . . . . . . . . . . 106
6.4 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106

7 Conclusions 109

A Appendix - Papers published 111

Bibliography 119
Chapter 1

Introduction

In the last decades soft matter has emerged as an important subfield of condensed
matter physics. The term describes a rich variety of different substances whose
common feature is that their properties are much more sensitive to mechanical
stresses and thermal fluctuations than hard materials such as aluminium or sodium
chloride. The predominant physical behaviour of soft materials occur at an energy
scale comparable with thermal energy at room temperature, where quantum effects
are unimportant. Nature’s main materials come from soft matter; most biological
materials such as blood, muscles, proteins/DNA, milk, and leaves are classifiable as
soft matter. Soft materials can also be important in a wide range of technological
applications. Since antiquity humans have used animal and plant fibres for their
basic needs such as clothing and writing (papyrus, pergamon, and paper). Today one
can find soft materials as structural and packaging materials, foams and adhesives,
detergents and cosmetics, paints, food additives, lubricants, and fuel additives.
Perhaps the most fascinating aspect of soft matter is the interesting behaviour
that arises in ways that cannot be predicted, or is difficult to predict, directly from its
atomic or molecular constituents. This is often because soft matter self-organises
into mesoscopic physical structures that are much larger than the microscopic scale
(the arrangement of atoms and molecules), and yet are much smaller than the macro-
scopic dimensions of the material. In particular some of the microscopic factors
can include a large number of internal degrees of freedom, weak interactions be-
tween structural elements, and a delicate balance between entropic and energetic
contributions to the free energy. These properties lead to large thermal fluctuations,
a wide variety of structural forms, sensitivity of equilibrium structures to external
conditions, macroscopic softness, and metastable states. The overall properties and
interactions of these mesoscopic structures determine the macroscopic behaviour of
the material. For example, the Indians of the Amazon basin collect the sap from a

1
1.1 Polymers 2

Figure 1.1: The figure shows screenshots of two types of polymers from computer
simulations. (a) Linear polymer composed by 200 monomers; (b) a star polymer
composed by 64 arms and 100 monomers per arm.

hevea tree and place it on their foot. After letting it dry for a short period of time, the
material becomes a boot. From microscopic perspective the starting point is a set of
independent, flexible polymer chains. The oxygen from the air builds in a few bridges
between the chains, which transforms the material from the liquid state to a network
structure which can resist tension. This material is known as rubber. Hence, soft
matter is an exciting field in which even a mild chemical action can induce drastic
changes on the properties of the material.
This thesis is devoted to the study of the self-organisation of some soft-matter
systems. Two types of systems are studied here: polymers and colloidal monolayers.

1.1 Polymers
Polymers represent one of the outgrowths fields in soft matter. They are polyatomic
molecules composed by small building blocks (a group of atoms), called monomers.
The most fundamental topology of polymeric structure is a linear chain as seen in
Fig. 1.1(a). One can generate new topologies by tethering the one end of chains to a d
dimensional surface, for example d = 0 (point) creates a star polymer Fig. 1.1(b) and
d = 2 (surface) creates a brush. To tether a chain at a two-dimensional surface is done
with a chemical bond, whose monomer-surface interaction strength is U À kT . One
such bond is strong enough to keep the rest of the chain tethered on the surface and
significantly reducing its mobility. This is a type of adsorption called chemisorption.
1.1 Polymers 3

Figure 1.2: (a)-(c) AFM images of linear polybutadiene (molecular mass 78.8kg/mol)
showing the patterns created after good-to-bad solvent transition occurs on ad-
sorbed of a thin film polymers on a mica surface. The surfave covergage for each
is Γ = 4.05 × 10−3 , 7.75 × 10−2 , and 4.01 × 10−1 mg/m2 respectively. (d)-(f ) Cluster-
height distributions correspoding to images (a)-(c), respectively. Pictures courtesy of
Emmanouil Glynos.

Nevertheless, one can have an adsorbed polymer on a surface without tethering it.
This can be achieved when the monomer-surface interaction strength is U ∼ kT ,
meaning that these monomer-surface contacts can easily break. Adsorption occurs
due to many monomer-surface interactions. The resulting conformational relaxation
of the polymer is driven by the competition between the entropic due to loss of
conformational freedom, and the drop in energy from binding monomers to the
surface. This type of adsorption is called physisorption. Polymer physisorption from
dilute solution has been frequently studied in the past, but to the best knowledge
of the author no previous studies have focused on the pattern formation of the
physisorbed polymers from a good solvent-to-bad solvent quenching transition. In a
collaboration with E. Glynos and V. Koutsos of the School of Engineering of University
of Edinburgh, patterns have been observed with atomic-force microscopic (AFM), in
which two types of polymers were studied, linear [1] and star polymers [2]. The AFM
images, in case of linear polymers, reveal a bimodal cluster distribution under certain
experimental conditions, see Fig. 1.2. Like in the Amazonian boots example above it
is easy to imagine what is happening. Before the good-to-bad solvent transition, the
chain spread on the surface to maximise their monomer contacts with the surface.
Additionally being in good solvent conditions the monomer-solvent interaction is
1.1 Polymers 4

Figure 1.3: High-contrast AFM images in air, 1 × 1µm2 , showing the patterns created
after good-to-bad solvent occured at adsorbed star polymers on a mica surface. From
image (a) to (c) the adsorbed amount is 0.104, 0.304 and 1.75 mg/m2 , respectively.
Pictures courtesy of Emmanouil Glynos

attractive, which makes the chain soluble. However, once entered into bad-solvent
conditions the monomer-solvent interactions becomes repulsive. Hence, the chain
collapses into a structure that minimises the surface contact with the solvent. For
low surface density each chain behaves as if it was an isolated chain, since it does
not feel the presence of the other chains. Therefore once the good-to-bad solvent
transition occurs each chain will collapse into itself leading to a cluster distribution
dominated by single collapsed chains. Nevertheless, for higher surface density, an
extra entropic term affecting the chain conformation is needed, which describes the
competition for space between different chains. When the the good-to-bad solvent
transition occurs at high surface density the chains are already close to each other
by having monomer-monomer contacts or even entanglements for long chains, and
that leads to the creation of many-chain clusters. One should expect that there is an
intermediate regime in which both clusters and single collapsed chains are observed.
In chapter 3 we demonstrate that this type of distribution can be reproduced with
computer simulations and we rationalise the observed AFM structures on the basis
of the polymer structures prior to the quench.
AFM experiments have also been performed with star polymers, see Fig. 1.3. Star
polymers are a special case of branched polymers where a star is composed by f
flexible polymer chains tethered to a core. f is called functionality. The functionality
governs the star’s behaviour from a linear chain for f = 1 and 2 to a colloidal particle
for f À 1. In other words, a star polymer is a hybrid between polymer-like objects
and colloidal particles, hence bridging two different domains of physics. A great
interest has been evoked recently on how stars behave in the proximity of a substrate.
For example it is interesting to understand how stars can act as depleting agents
of colloidal particles, in other words to prevent colloidal aggregation and with an
1.2 Scale-free neighbour networks in polydisperse 2D fluids 5

Figure 1.4: Three examples of the kinds of scale-free networks. (a) A vizualization
of the network structure of the Internet at the level of autonomous systems. (b) A
map of interacting proteins. (c) A social network, in the case of sexual contacts. The
images were taken from the Refs. [6, 7].

ultimate goal to assemble the colloids into ordered structures [3, 4, 5]. However, it
is still an unexplored region on how star polymers behave in the proximity of an
attractive surface. In chapter 4 we discuss how a surface can affect the conformation
of a physisorbed star. Measurements from computer simulations of the fraction of
monomers bound to the surface, height, radius of gyration, and asphericity provide
valuable insights on a star polymer’s conformations. We rationalise on the basis of
the results and it will allow us to map a star’s behaviour (from linear to soft-colloid)
based on the number of arms and their length, and the properties of the surface. The
mapping the behavior of an adsorbed star polymer on a surface provides us valuable
insights and can act as a guide to predicting a star’s conformation on a surface for
future experiments.

1.2 Scale-free neighbour networks in polydisperse 2D


fluids

Polydisperse hard-disk fluids are of considerable interest as model of soft matter


systems, for example, as models of colloidal monolayers, froths and foams, and
of packing and segregation in granular materials. In particular we focus on the
neighbour network of a two-dimensional polydisperse hard-disk fluid with a power
1.3 Colloidal monolayers with dipolar interactions 6

law diameter distribution. The aims are twofold. First we want to understand how a
diameter distribution with a slowly decaying tail, as it happens to power laws and
in contrast with exponential distributions, will affect the neighbour network. It is
tempting to speculate that if the diameter distribution follows a power law, then
perhaps the network distribution will also vary in a similar way. The assumption is
that for any given disk the number of immediate neighbours will be proportional to
its circumference and hence its diameter. And second if the neighbour network does
vary with a power law then does it also have the properties of scale-free networks?
Scale-free networks are characterised in qualitative terms by a small number of highly
connected vertices called “hubs” and a large number of low connected vertices, see
Refs. [6, 7]. Some examples of real scale-free networks are illustrated in Fig. 1.4. The
degree distribution (i.e. the probability of finding a vertex with k connections) varies
with a power law, a necessary but not sufficient condition for a network to be scale-
free. Many physical systems have been identified as scale free, for example the World
Wide Web, the Internet, metabolic and protein-protein interactions, sexual contacts,
collaborations among scientists. But what makes scale-free networks fascinating is
that they have self-similar behaviour. For example, in a self-similar network where the
vertices are connected with edges (connections of links) there is no possible way to
assess whether a vertex has an above or below average number of connections.1 This
happens because power law distributions with slow decaying tails have infinite mean,
thus there is no characteristic scale to use for comparison. In chapter 5 we examine
the polydisperse hard-disk fluid by using constant-pressure Monte Carlo simulations.
Additional measurements are discussed in the chapter such as the assortativity of
the network, which is found to be positive, meaning that vertices of equal degree are
connected more often than in a random network. Finally, the equation of state is
determined and compared with the prediction from a scaled-particle theory.

1.3 Colloidal monolayers with dipolar interactions


In the final part of the thesis, we look at two-dimensional binary mixtures of dipolar
colloids. A popular description of colloids is that they are particles with the simplest
and highest possible symmetry (sphere), and without any additional structure on the
mesoscopic length scale, see Fig. 1.5. It is possible experimentally to insert within
the colloid a magnetised substance and thus effectively create a colloid carrying a
point magnetic dipole. The importance of this is for example creating new type of
polymers where its monomers are colloids; or one can use external fields and take
1
A finite size network will be bounded by a minimum and maximum degree, which can give a finite
mean. The self-similarity manifests between the bounds.
1.4 Summary 7

Figure 1.5: Optical micrograph of a monolayer of polystyrene spheres, with diameter


2.7µm, at the interface between water and a mixture of decane and undecane in the
through. The picure is taken from the Ref. [8].

advantage of the long range repulsive forces (from dipole-dipole interactions) to


create well disperse colloidal particles in the substance of interest. In chapter 6 we
are interested in what are the global minimum-energy configurations of a binary
mixture of dipolar colloids confined to a flat interface, and with a magnetic field is
applied perpendicular direction polarising the particles and inducing long range
repulsive interactions between them. We use genetic algorithms to efficiently search
the global minimum of energy landscapes; genetic algorithms are described in the
methodology of chapter 6.

1.4 Summary
This thesis is organised as follows. In chapter 2 we briefly summarise key concepts in
statistical mechanics, computer simulations, polymers and fractals that underpin
this thesis. In chapters 3 and 4 we study the self-assembly of physisorbed linear and
star polymers, respectively. In chapter 5 we look at the behaviour of the neighbour
network of a two-dimensional polydisperse hard-disk fluid with slow decaying diam-
eter distribution. In chapter 6 we examine ordered equilibrium structures formed
by binary mixture of anisotropic dipolar particles confined on a plane, under the
presence of an external magnetic field. Finally, in chapter 7 we conclude this thesis.
Chapter 2

General Considerations

Science is the systematic observation and understanding of Nature. Until recently


there were two ways one could understand Nature. The first was to perform experi-
ments, for example by recording the time for a falling apple from different heights to
hit the ground. The second method is by developing a theory. Theory takes math-
ematics and constructs a framework in which a model can be built and studied.
Thus, in the case of a falling apple (or more precisely the orbits of planets) Newton
developed the theory of gravity, which explains how the apple falls, and planets orbit
around the sun rather than crushing each other. Theories can be tested by comparing
their predictions with experimental results. Disagreement between experimental
results and theoretical predictions can lead to a new theory, as happened in the 19th
century when Mercury’s peculiar trajectory was first observed and led to Einstein’s
theory of general relativity.
The development of computers has provided an alternative mode of research
in science. Computer simulations can be used as a linking bridge between theory
and experiments. Mathematical in nature, computer simulations provide a new
metaphor for the laws of Nature, the algorithms. The first systematic explorations
with computers occurred in 1952, with Metropolis being interested in having the
Los Alamos MANIAC machine tried against a wide spectrum of mathematical and
physical problems. However, simulations, or to be more accurate algorithms, which
are the heart of computer simulations, are not new discoveries. The ancients used
algorithms to gain insights into difficult mathematical or physical problems; one
example is the Euclidean algorithm, which determines the greatest common divisor
in any Euclidean domain (i.e. integers). Simulations can easily examine different
theories and visualise the results thus providing valuable insights. Furthermore,
they can aid in interpreting experimental results, and in devising new experimental
strategies.

8
2.1 Statistical physics 9

In the case of many-body problems, computer simulations of condensed-matter


systems frequently use statistical mechanics. Statistical mechanics is the discipline
that connects the microscopic variables (positions, momenta, and interactions) of
a physical system to its macroscopic ones (temperature, pressure, etc.). Many sim-
ple problems in statistical mechanics are exactly solvable, but only a handful of
non-trivial problems can actually be solved exactly. Other problems can be tack-
led by using successive approximations, and perturbative expansions; computers
play an important role in such work, for instance in calculating virial coefficients,
understanding polymer conformations, and so on.
Polymer physics is founded upon the principles of statistical mechanics, which
studies the structural and dynamical properties of polymers. It is a relatively old
field (starting in 1920), but since then it has become a fundamental part of statisti-
cal mechanics providing great insights into understanding polymers like DNA and
designing new exotic materials. One of these insights was that polymers are finite
fractals, which corresponds to geometrical objects whose geometry is invariant on
all scales.
In this chapter we briefly summarise the key concepts in statistical mechanics,
computer simulations, polymers and fractals that underpin this thesis.

2.1 Statistical physics


Statistical mechanics is a probability theory which provides mathematical tools
for dealing with systems of many particles. It is able to predict statistics (averages,
fluctuations) for the macroscopic properties (such as for instance, pressure and
temperature) of a many-body system from its microscopic properties, such as inter-
actions.

2.1.1 Ensembles
Statistical mechanics groups many-body systems into ensembles. An ensemble in
statistical mechanics consists of a very large (theoretically infinite) number of copies
of a system, all characterised by the macroscopic varibles. There are four ensembles
that are commonly used. (a) The micro-canonical ensemble is a group of systems
characterized by a fixed number of particles N , total energy E , and in volume V .
This ensemble is often denoted as the NV E ensemble and consists of copies of an
isolated system. (b) The canonical ensemble consists of many-body systems with
equal number of particles N , which are at thermal equilibrium with a heat bath at
temperature T , and at the same volume V . This ensemble exchanges energy with the
2.1 Statistical physics 10

heat bath and is denoted as the NV T ensemble. (c) The grand-canonical ensemble
is a collection of identical systems at equilibrium with an external reservoir with
which they exchange both energy and particles. This ensemble is refered to as the
µV T ensemble, where µ is the chemical potential controlling the average in the
number of particles. (d) In the isothermal-isobaric ensemble, all the systems have
the same number of particles N and maintain the same temperature T and pressure
P . It is refered to as the N P T ensemble and it plays an important role in chemistry
as many chemical systems are prepared and studied under conditions of constant
temperature and pressure.

2.1.2 Time averages and ensemble averages

The microscopic states (positions r and momenta p) of a many-particle system can be


represented in phase space. In the case of a three-dimensional system of N particles,
the values assumed by the variables rN and pN at any time define a point in the
6N -dimensional phase space. A set of points in phase space linked by dynamical
equations of motion define a trajectory.
If A rN , pN is a function of the 6N coordinates and momenta, its time average
¡ ¢

over a period τ is defined as

1
Z τ£
A rN , pN dt
¡ ¢¤
〈A 〉t = lim (2.1)
τ→∞ τ 0

A different averaging procedure based on the concept of ensemble can also be intro-
duced. The average properties of a system can be obtained from a single “snapshot”,
rather than tracking the system’s configurations through time. Hence, we use a func-
tion describing the distribution in phase space at time t of the phase points relative to
a certain statistical-mechanical ensemble. This function is called probability density,
f rN , pN , t . Under equilibrium conditions f is independent of time and ensemble
¡ ¢

averages can be defined as follows


ZZ
A rN , pN f rN , pN , t d rN d pN
¡ ¢ ¡ ¢
〈A 〉e = (2.2)

If the average in eq. 2.1 is performed over a long time, and the system eventually
flows through all its possible microstates, then the ensemble averages become the
same as the time averages, that is

〈A 〉t = 〈A 〉e (2.3)

This equivalence is known as the ergodic theorem and it is believed to hold for all
2.2 Simulation Techniques 11

many-body systems in Nature.

2.2 Simulation Techniques


In this section, we discuss a few computational tricks that are of great practical
importance for an efficient simulation program. Additionally, we discuss some fun-
damental concepts in computer simulations such as how Monte Carlo and molecular
dynamics algorithms work.

2.2.1 Interaction potentials

We describe our model of the system of interest by a function which gives the po-
tential energy for a given configuration of the particles in the system. Usually, the
assumption is made that the potential is pairwise additive. That is, we assume that
the total potential is just the sum of potential for each pair of particles, which is
expressed as a function of their relative positions (and possible orientations). This
is justified because three-body (or higher order) terms in the potetial give a small
contribution into the description of the overall system. More details can be found in
Refs. [9, 10].
Perhaps the simplest model of a particle is to regard it as an impenetrable hard
sphere and it is represented by the potential
(
∞ r <σ
U (r ) = (2.4)
0 r >σ

where r is the distance between the particles and σ is the particle diameter. The
hard core interaction which prevents the particles from overlapping provides a good
representation of the Pauli repulsion which operates at short distances and has its
origin in the exclusion principle. Another, widely used pair potential is the Lennard-
Jones potential,

σ 12 ³ σ ´6 ¸
·³ ´
U (r ) = 4ε − (2.5)
r r
where r is the distance between the particles, σ is the distance parameter and ε is
a parameter giving the depth of the minimum in the potential. At large distances,
this has the asymptotic 1/r 6 dependence of the van der Waals interaction, and the
1/r 12 term approximately describes the hard-core repulsion when the particles come
close together. This potential provides an excellent description for argon and it is
frequently used for many other molecules.
2.2 Simulation Techniques 12

Figure 2.1: The diagrams display the the hard-sphere potential (top) and Lennard-
Jones potential (bottom).

For short-range potentials, we can truncate the potential at a certain distance


beyond which the interactions are negligible. This means that any two particles
further apart than this distance do not need to be considered when calculating the
total potential energy, speeding up the simulation. The discontinuity in the potential
can cause problems, however. A discontinuous potential means an infinite force
(since F = −∇U ), which can lead to numerical instabilities. One way to avoid this is to
shift the potential in the vicinity of the cut-off by a function which brings it smoothly
to zero.

2.2.2 Reduced Units

When carrying out a computer simulation it is convenient to define a set of reduced


units in terms of the potential parameters of the system under study. For example,
for Lennard-Jones fluid, with the pair potential given in Eq. 2.5, distances can be
expressed in terms of the parameter σ, and energies can be expressed in terms of ε.
We also use the mass of the particles in the system as a fundamental unit (i.e. m = 1).
From these fundamental definitions, we can obtain other quantities in reduced units.
Some reduced units for the Lennard-Jones potential are listed in Table 2.1.
The most important reason for using reduced units is that there are many different
states in real units that corresponds to the same state in reduced units. The use of
reduced units means we do not have to repeat the simulation for each of these states.
Another advantage is that values in reduced units will be of order unity, hence we
2.2 Simulation Techniques 13

Table 2.1: Properties of Lennard-Jones system in reduced units.

Quantity Reduced Unit


Distance r ∗ = r /σ
Density ρ ∗ = ρσ3
Energy E ∗ = E /ε
Temperature T ∗ = k B T /ε
Pressure P ∗ = P σ3 /ε
Time t ∗ = (ε/mσ2 )1/2 t

avoid the potential problems of using the very small numbers of atomic systems on a
computer. The use of reduced units also simplifies the potential, allowing us to set
the parameters of the potential to one. We do not need to choose specific values of
these parameters.

2.2.3 Periodic Boundary Conditions


In a simulation of finite number of particles, a significant fraction of particles will be
at the edges of the system. The environment of these particles will be very different to
the environment of a particle within the bulk system. In order to reduce this problem,
periodic boundary conditions are normally employed. We make copies of the system
in all directions, see Fig. 2.2. When a particle leaves the central simulation cell at
one side, its periodic image enters from the other side, thus conserving the number
of particles in the central simulation cell. Technically, every particle interacts with
every particle in all cells, but often the minimum image convention is used. When
calculating the force and the interactions on a pair of particles, the only interaction
that is considered is that due to the nearest of the periodic images of the particular
particle.

2.2.4 Monte Carlo


Monte Carlo methods aim to generate a trajectory in phase space which samples
from a chosen statistical-mechanical ensemble. The ensemble average of a certain
quantity A is then calculated via

1X
〈A 〉 = Ai exp(−βE i ) (2.6)
Q i

exp −βE i is the partition function, β = 1/k B T and exp −βE i is the
P ¡ ¢ ¡ ¢
where Q = i
Boltzmann factor which weights every accessible state i of energy E i . However, the
2.2 Simulation Techniques 14

Figure 2.2: Schematic illustration of periodic boundary conditions.

number of accessible states in a large system can be huge thus making the exact
evaluation of the average in eq. 2.6 unfeasible with current computers. Moreover,
certain states (those with small Boltzmann factor) contribute very little to the average,
and hence should be omitted in an efficient calculation. To overcome these problems,
importance-sampling is employed. In this scheme the only configurations to be
sampled are those that make a significant contribution to the partition function
and ensemble averages. This task is achieved by generating a Markov chain of
configurations in which each state is generated by “perturbing” the preceding one in
the chain, and accepted as a new configuration only if the detailed balance condition
is satisfied.

A sufficient (but not necessary) detailed-balance condition is that for old (o) and
new n states
J (o → n) = J (n → o) (2.7)

where J (o → n) is the probability flux from a state o to a new state n during a given
simulation step. The flux J (o → n) can be factored into three terms

J (o → n) = p (o) · α (o → n) · acc (o → n) (2.8)

where p (o) is the probability of being in state o (which at equilibrium should follow
the Boltzmann distibution), α (o → n) is the probability of generating the trial move
from o to n, and acc (o → n) is the probability of accepting the trial move from o and
n. By combining eqs. 2.7 and 2.8 the detailed-balance condition can be rewritten as

acc (o → n) acc (n → o) p(n)


= · (2.9)
acc (n → o) acc (o → n) p(o)
2.2 Simulation Techniques 15

p(n)
where p(o)
is obtained based on the statistical ensemble we work on. In the case of
NV T ensemble the ratio can be expressed as the Boltzmann factor of the energy
difference:
−1 −βE (n)
p(n) Z NV T e
= −1 −βE (o) = e −β[E (n)−E (o)] (2.10)
p(o) Z NV Te

where E (n) and E (o) are the system energies for the new and old state, respectively.
Z NV T is the partion function defined as the sum of all the energy states, E i , and
read as Z NV T = e −βE i . Now if we assume that α (o → n) = α (n → o), then eq. 2.9
P

becomes ³ ´
acc (o → n) = min 1, e −β[E (n)−E (o)] . (2.11)

A typical importance-sampling Monte Carlo scheme to perform a simulation


in the canonical (NV T ) ensemble will proceed as follows. The system is prepared
in some initial configuration. A particle is chosen randomly and displaced within
the simulation cell. If the trial move results in a decrease of the system energy, then
the move is accepted and the particle positions updated. If the trial move results
¡ ¢
in an increase of energy, instead, the move is accepted with probability exp −β∆E ,
where ∆E is the difference in system energy associated with the trial move. This
is implemented in a computer simulation by generating a random number in the
interval (0, 1) and accepting the move only if the random number is less than the
¡ ¢
value exp −β∆E . These steps are repeated for the subsequent randomly chosen
particles. After a large number of trial moves, simple unweighted averages over
the visited states can be calculated since each state is sampled with a probability
proportional to its Boltzmann factor.

2.2.5 Molecular dynamics


Molecular dynamics (MD) simulations is a classical technique to compute equilib-
rium structural and dynamical properties of a many-body system.
In this technique each particle moves according to Newton’s laws of motion,
which are integrated numerically. The positions and velocities of the particles are
updated every time-step and the equations of motion integrated to generate a trajec-
tory in phase space. This procedure is repeated for a number of time-steps required
to equilibrate the system and calculate accurate time averages.
A typical MD simulation will proceed as follows: positions ri and velocities vi of
the particles at time t are stored in the computer. The force acting on each particle
is calculated from the potentials (Fi = −∇i U ) and then the equation of motion,
Fi = m i ai , is integrated over a finite time-step ∆t according, for instance, to the
Verlet algorithm to get the position of the particles in the next time-step, t + δt [9]
2.2 Simulation Techniques 16

ri (t + δt ) = ri (t ) − ri (t − δt ) + ai (t )δt 2 (2.12)

The velocities are calculated separately from the positions as follows:

ri (t + δt ) − ri (t − δt )
vi (t ) = (2.13)
2δt

The numerical integration of the equations of motion using the Verlet algorithm and
its variants generates errors of order δt 4 in the positions and δt 2 in the velocities.

A better integration algorithm is the so-called “velocity-Verlet”, which computes


more accurately the velocities (the errors is of order δt 4 ) and it reads as

1
ri (t + δt ) = ri (t ) + vi (t )δt + ai (t )δt 2 (2.14)
2

1
vi (t + δt ) = vi (t ) + [ai (t ) + ai (t + δt )] δt . (2.15)
2
The original Verlet algorithm may be recovered by eliminating the velocities. The
algorithm only requires storage of ri , vi and ai and its implementation involves two
stages, with the force evaluation in between. First, the new positions at time t + δt
are calculated using eq. 2.14 and then the forces and accelerations at time t + δt
are computed. At this point the velocities at time t + δt are available. The origin of
eq. 2.15 comes by calculating the velocities at mid-step i.e. at time t + 21 δt

1 1
vi (t + δt ) = vi (t ) + ai (t )δt (2.16)
2 2

and at time t + δt
1 1
vi (t + δt ) = vi (t + δt ) + ai (t + δt )δt . (2.17)
2 2
Combining eqs. 2.16 and 2.17, we obtain eq. 2.15.

Overall, the Verlet algorithms for most MD simulations are perfectly adequate.
The success of Verlet algorithms relies on their simplectic character, meaning that it
has a time-reversal symmetry and long-term energy conservation.

In a standard MD simulation total energy and momentum are conserved quanti-


ties. A typical MD program simulates a microcanonical ensemble (constant NV E ).
MD simulations can also be performed in constant-temperature ensembles, such
as NV T (canonical ensemble), and N P T (where P is the system pressure). In these
cases the temperature T is kept constant by coupling the system to a heat bath. A
detailed review of constant-temperature MD methods is given in Refs. [9] and [11].
2.3 Simulation Techniques 17

2.2.6 Brownian dynamics

An alternative simulation technique that keeps the system temperature constant is


Brownian dynamics (BD).

In the presence of large time-scale separations between the rapid motion of


the solvent and the slower motion of the solute, such as in the case of polymers,
amphiphile and colloidal suspensions, the simulation time can became prohibitively
long. In fact, the short time steps needed to capture the fast motion of the solvent,
and the long runs needed to study the structural evolution of the solute, can make
simulations very time consuming, especially in those cases in which the fast solvent
modes are not of interest. BD is a mesoscale simulation technique in which solvent
particles are replaced by a combination of stochastic and frictional forces.

At the very core of this technique there is the integration of the Langevin equation
in order to generate trajectories of the solute particles in which we are interested,
letting friction and random terms to mimic the solvent interactions with the solute.
The Langevin equation in this situation is written

Fi = −∇i U − ξm i vi + Wi (2.18)

where vi is the velocity of particle i , U is the total potential energy, ξ and Wi are
the friction coefficient and the random force representing the effects of the solvent.
The random force is, in a typical BD simulation, Gaussian noise, which obeys the
fluctuation-dissipation theorem

〈Wi (t )〉 = 0
〈Wi (t ) · W j (t 0 )〉 = 6mk B T ξδi j δ(t − t 0 ). (2.19)

The Langevin equation 2.18 can be integrated numerically, for example using
a Verlet-like algorithm. The friction coefficient ξ is related to the single-particle
diffusion coefficient D accordingly to Einstein’s equation

kB T
ξ= (2.20)
mD

where k B is the Boltzmann’s constant and m is the mass of the diffusing particle.

Hydrodynamic effects, that is the influence of one particle on another through


the flow of the solvent around them, and the interaction between two particles
due to solvent structure, can be included in this simulation scheme. Details are in
Refs. [9, 12, 13].
2.3 Polymers and Scaling Theory 18

2.3 Polymers and Scaling Theory


The development of human civilisation has been dictated by the availability of mate-
rials. In fact, the discovery of a new material can have such drastic effects as to lead
to the decline of an old civilizations and give the rise to a new one. For this reason
history is divided into eras named after the primary materials used; the Stone Age,
the Bronze Age, and the Iron Age. Similarly, we can say that in the 20th century we
entered the Polymer Age.
In this section we will discuss the definition of a polymer, and review some
universal properties of linear chains.

2.3.1 Definition and structure


Polymers are macromolecules (polyatomic structures) consisting of many elementary
units, called monomers, and they are connected to each other by covenant bonds.
The entire structure of a polymer is generated through the process of polymerisation,
the process by which elementary units are covalently bonded together. The number
of monomers in a polymer molecule is called the degree of polymerisation, N . For
example, polyethylene’s repeating unit is −CH2 −CH2−, since the monomers used in
their synthesis are ethylene, CH2 =CH2 , see Fig. 2.3.
The definition of a polymers is generic and includes a huge variety of polymers
with distinct structural and architectural features, such as DNA and polypetides;
these features change the physical properties of the molecules. For instance both the
boiling point and the melting point increase rapidly with the number of backbone
monomers. We briefly describe some of the ways of categorising these structures. The
first way of categorising a polymer is by the number of different types of monomers
in the molecule. If a polymer contains only one type of monomer, then it is called a
homopolymer, otherwise it is called a heteropolymer. Heteropolymers have a whole
range of subcategories depending on the number of different types of monomers
and their position in the molecule. For example, for two types of monomers, say
A and B, then you can have different sequences of monomers, e.g. alternating ...-
A-B-A-B-A-B-A-..., random ...-A-A-B-B-B-A-B-..., diblock ...-A-A-A-B-B-B-... chains.

Figure 2.3: Polymerization of polyethylene monomers.


2.3 Polymers and Scaling Theory 19

Figure 2.4: Examples of polymer architectures (a) linear; (b) ring; (c) star (d) H; (e)
comb; (f) ladder (g) dentrimer; (h) randomly branched.

The second was by which one can categorise polymers is by their size. Oligomers
are polymers consisting of a small number of monomers (generally, less than 20);
polymers may contain between 20 and 10 billion (for the longest known chromo-
some) monomers. Third, another important way of characterising of polymeric
systems is by their architecture. Types of polymer architectures include linear, ring,
star-branched, H-branched, comb, ladder, dendrimer or randomly branched, see
Fig. 2.4. The properties of branching and the formation of networks (via a high degree
of crosslinking) make polymers useful as soft solids (e.g. erasers, tyres).

2.3.2 Polymer conformations

To understand the thermodynamic and dynamical properties of polymers, one has to


look first to the possible conformations. The simplest model that describes a linear
polymer is a freely joined chain. The model represents the polymer as a chain of n + 1
identical monomers with a constant bond length |ri | = l , see Fig. 2.5. Moreover, we
make an assumption that the chain is in an ideal state, meaning that there are no
interactions between the monomers separated by a large number of bonds along the
chain, so that |i − j | À 1.
We define the end-to-end vector, which is the sum of all n bond vectors ri in the
chain:
n
X
Rn = ri (2.21)
i =1

Different configurations of the chain will have different bond vectors and hence
different end-to-end vectors. However, the ensemble average of Rn over all possible
states by either considering many chains or many different configurations of the
2.3 Polymers and Scaling Theory 20

Figure 2.5: Schematic illustration of a conformation of a linear polymer.

same chain, is zero


〈Rn 〉 = 0 (2.22)

which signifies that there is no preferred direction in this ensemble. The simplest
non-zero average is the mean-square end-to-end distance:
*Ã ! Ã !+
n n n X
n
〈R 2 〉 =
X X X
ri · rj = 〈ri · r j 〉 (2.23)
i j i =1 j =1

If all bonds have the same length l = |ri |, then the scalar product can be represent
in terms of the angle θi j between bond vectors ri and r j

ri · r j = l 2 cos θi j (2.24)

The mean-square end-to-end distance becomes a double sum of average cosines:

n X
n ­
〈R 2 〉 = l 2 cos θi j
X ®
(2.25)
i =1 j =1

In the freely joined chain model there are no correlations between the directions
of different bond vectors, thus cos θi j = 0 for i 6= j . There are only n non-zero terms
­ ®

in the double sum (cos θi j = 1 for i = j ). Therefore, 〈R 2 〉 of a freely joined chain is


quite simple:
〈R 2 〉 = nl 2 (2.26)

However, in a typical polymer chain, there are correlations between bond vectors
(especially between neighbouring ones), so 〈cos θi j 〉 6= 0. So one can group these
2.3 Polymers and Scaling Theory 21

Figure 2.6: Schematic illustration of mapping a linear chain (continuous line) to an


ideal flexible chain composed by effective bond of Kuhn length, b.

correlations into one quantity

1X n X n ­
cos θi j
®
Cn = (2.27)
n i =1 j =1

where the coeffiecient C n , called Flory’s characteristic ratio, is the average value of
the nj=1 cos θi j over all main-chain bonds of the polymer. Now eq. 2.25 can be
P ­ ®

reduced to
n X
n ­
〈R 2 〉 = l 2 cos θi j = C n nl 2
X ®
(2.28)
i =1 j =1

All real polymers have C n > 1, meaning that the local correlations are significant
i.e. cos θi j 6= 0, which means that the local alignment of the bonds favours a
­ ®

parallel orientation. The physical origins of these local correlations between the
bond vectors are restricted bond angles and steric hindrance. All models of ideal-
chain polymers ignore steric hindrance between monomers separated by many
bonds. This has as a result for a chain with large numbers of main chain bonds
(n → ∞) their characteristic ratios to saturate C ∞ = limn→∞ C n . Thus, 〈R 2 〉 can be
approximated for long chains by

〈R 2 〉 ∼
= C ∞ nl 2 (2.29)

The values of the characteristic ratios of some common polymers are listed in Ta-
ble 2.2.
The Flory characteristic ratio allows a simple description of all ideal polymers by
an equivalent freely joined chain. The equivalent chain has the same mean-square
end-to-end distance 〈R 2 〉 and the same maximum end-to-end distance R max as the
actual polymer, but has N freely-joined effective bonds of length b, see Fig. 2.6. This
2.3 Polymers and Scaling Theory 22

Table 2.2: Characteristic ratios, and Kuhn lengths for common polymers

Polymer Monomer C∞ b (Å)


1,4-Polybutadiene (PB) −(CH2 CH=CHCH2 )− 5.3 9.6
Poly(ethylene oxide) (PEO) −(CH2 CH2 O)− 6.7 11
Atactic polystyrene (PS) −(CH2 CHC6 H5 )− 9.5 18

effective bond length b is called the Kuhn length. Therfore, the Kuhn length for an
equivalent freely joined chain is given by

〈R 2 〉 C ∞ nl 2
b= = (2.30)
R max R max

where R max is the contour length of the equivalent freely joined chain.

Eq. 2.30 renormalizes the monomers, and holds for all flexible linear polymers in
the ideal state (N À 1), with all chemical-specific characteristics contained within
the Kuhn monomer (i.e. Kuhn length). This makes the properties of flexible polymers
independent of the local chemical structure, and thus universal.

2.3.3 Solvent effects

A polymer in solution is interacting with the solvent molecules. These interactions


can significantly alter configuration of the polymer. There are three types of solvents,
good-solvent, ideal (or θ-solvent) and bad-solvent. In good solvent conditions the
interactions between the solvent molecules and the polymer monomers are attrac-
tive. This means that the polymer is soluble and the effective monomer-monomer
interaction is repulsive. The chain conformation can be described as a self-avoiding
walk, which is a random walk on a lattice that never visits the same site more than
once. In an ideal solvent the net interaction between solvent molecules and polymer’s
monomers is zero. The polymer conformation resembles a random walk.1 In the case
of the bad-solvent conditions we have an attractive effective monomer-monomer
interaction and the polymer collapses into a globular configuration for minimising
the surface contact between the polymer and solvent.

1
The monomers of a real chain in ideal-solvent do not overlap, but the statistics of the chain are
the same with that of a random walk.
2.3 Polymers and Scaling Theory 23

2.3.4 Scaling concepts of polymers

Flory Theory for a single chain

A simple and excellent scheme was devised by Flory for obtaining valuable insights
on the conformations of linear chains. We briefly describe his method here, for more
details see Refs. [14, 15].

Consider a polymer of N Kuhn monomers in good solvent conditions, which


are uniformly distributed within volume R d with no correlations between them.
Note that the argument holds for an arbitrary dimensionality d . The probability of
a second monomer being within the excluded volume v (in good solvent v > 0) of
a given monomer is the product of the excluded volume v and the number density
of the monomers in the pervaded volume of the chain N /R d . The energetic cost of
being excluded from this volume is kT per exclusion of kT v N /R d per monomer. For
all N monomers in the chain, this energy is N times larger

N2
F int ≈ kT v (2.31)
Rd

The Flory estimate of the entropic contribution to the free energy of a real chain is
based on the fact that the entropic elasticity obeys the Hooke’s law, and thus it is
equal to the the energy required to stretch an ideal chain to end-to-end distance R:

R2
F ent ≈ kT v (2.32)
N b2

The total free energy of a real chain in the Flory approximation is the sum of the
energetic interaction and the entropic contributions:

N2R2
µ ¶
F = F int + F ent ≈ kT v d + (2.33)
R N b2

The minimum free energy of the chain (obtained by setting ∂F /∂R = 0) gives the
optimum size of the real chain in the Flory theory, R = R F :
à !
∂F N2 RF
= kT −d v d +1 + 2 =0
∂R R N b2
F
d 2 3
R Fd +2 ≈ vb N (2.34)
2

The Flory theory leads to a universal power law dependence of polymer size R F
2.3 Polymers and Scaling Theory 24

Figure 2.7: Stretching a linear chain by applying a force f at both ends of the chain.
The characteristic length ξ represents the region in which within it the chain statists
are unperturbed by the stretching.

on the number of monomers:

3
R F ∼ N ν with ν = (2.35)
d +2

where ν is the scaling exponent characterising the polymer conformation. It is


interesting to note that ν is independented of v, thus being a universal exponent.
One can work out with similar arguments the values of ν in different solvents, for
more details are in Ref. [15]. The other values of ν for d = 3 are 1/2 corresponding to
an ideal chain (or θ-solvent conditions where the excluded volume v = 0) and 1/3
describing the collapsed state of the chain when it enters into bad-solvent conditions.
The predictions of the Flory theory are in good agreement with both experiments
and other more sophisticated theories. However, its success lies on cancellation of
errors, because both the entropic and energetic terms in eq. 2.33 are overestimated.
Nevertheless, Flory theory is useful because it is simple and provides a reasonable
answer.

Stretching and blobs

To further understand scaling concepts, consider a chain of N Kuhn monomers of


b size, under tension. The stretching is done by applying a force of magnitude f at
both ends of the chain. In this problem the only characteristic lengths involved are
(a) the Flory radius R F , and (b) the length ξ = kT / f , which defines a tension blob of
size ξ containing g monomers each, such that on length scales smaller than ξ the
chain statistics are unperturbed, while on larger length scales the chain is a string of
independent blobs, see Fig. 2.7. The number of monomers per blob, g , is related to ξ
by the Flory law ξ ≈ bg ν .
2.4 Fractals and self-similarity 25

The end-to-end distance R f is the product of the tension blob size ξ and the
number of these blobs N /g

N f b 1/ν−1
µ ¶
Rf ≈ ξ ≈ Nb . (2.36)
g kT

This shows that a chain in good solvent (ν = 3/5) has an elastic response which is
nonlinear, 1/ν − 1 = 2/3, than in the case of an ideal chain (ν = 1/2). In both types of
solvents a stretched chain will have fewer possible configurations, but in good solvent
conditions it has fewer possible configurations to lose. For this entropic reason it
returns a smaller stretching force, but increases more rapidly with extension.
This concept of scaling, that is to divide a chain of Kuhn monomers into blobs
that each contribute of order kT to the free energy, further simplifies the problem at
hand.

2.4 Fractals and self-similarity


As demonstrated in section 2.3.1 polymers can adopt many different conformations
that due to their size (the largest DNA molecules has 1010 bonds) can span through
a wide range of length scales. But at the same time, they can be coarse-grained
to high degree without losing the overall structural information. There is another
feature in polymers that is related with the above characteristics, and that is most
polymers are self-similar, or finite random fractals. In this section we will explore
self-similar objects and some basic fractal properties by looking at polymers, and
other examples.

2.4.1 Fractal dimension and Koch curve


Any polymer follows the Flory law, eq. 2.35 R ∼ N ν , where ν takes the values 3/5, 1/2,
and 1/3 in three dimensions for good, ideal and bad-solvent conditions, respectively.
The values of ν characterise the conformations the chain takes, for example in a bad
solvent (ν = 1/3) the chain collapses into a globular structure. To explain this we
briefly look to a mathematical example.
Consider a regular fractal, called the Koch-curve, see Fig. 2.8. To generate it
one has to start with a section of a straight line and then divide it into three equal
subsections. Then on the top of the middle subsection an equilateral triangle is
drawn with its bottom side erased. Thus we end with four segments of equal length,
with total length 4/3. Iterating the process infinitely many times results in a curve of
infinite length, which is everywhere continuous but nowhere differentiable. Another
2.4 Fractals and self-similarity 26

Figure 2.8: On the left an illustration shows the Koch curve after different number
of iterations and on the right a display of the self-similar feature to a high order
approximation to the Koch curve. (Both images were taken from Google search with
related keywords)

striking feature is that if we magnify any section of the curve we will observe the same
structure, see Fig. 2.8. This is an example of a fractal.
To understand this further we consider the following example. We have an infinite
long straight rod of thickness (or diameter) H and it has uniform density. Now we
draw a sphere of radius r around the rod, as seen in Fig. 2.9(a) and ask the question:
how the amount of mass, m, within the sphere changes as function of the radius of the
sphere. When the sphere is much bigger than the thickness of the wire (r À H ) then
the rod is effectively an one-dimensional object and so m ∼ r . If however the sphere
is smaller than the thickness (or diameter) of the rod (r < H ) then the mass within
the sphere will scale with the volume, thus m ∼ r 3 . The dependence of the mass m
of the part of the wire inside the sphere of radius r is sketched in Fig. 2.9(a). Thus
we can say that the rod is one-dimensional on length scales much larger than its
thickness r À H and three-dimensional on smaller scales r < H . Another important
point to make is the relation between m and r in the form of m ∼ r D , where D is a
critical exponent (also called Hausdorff dimension).
Now we apply similar arguments for the case of the Koch curve. We plot two circles
of diameter 2r equal to the lengths of the lengths of two consecutive generations,
see Fig. 2.9(b). The radius of the circles changes by a factor of 3 (r 1 = 3r 2 ), while the
number of segments within the circles changes by a factor of 4 (n 1 = 4n 2 ). Similar
with the previous example we assume that the number of segments within a cicle is

n ∼rD (2.37)
2.4 Fractals and self-similarity 27

Figure 2.9: (a) The diagram shows how the amount of mass m of the part of the wire
inside the sphere of radius r as function of r . Both axes have logarithmic scales. (b)
Comparing the number of segments part of the Koch curve for two different circle
radius, r 1 and r 2 .

Now we can calculate the Hausdorff dimension in the following way:

n 1 = cr 1D = c(3r 2 )D (2.38)
n1 = 4n 2 = 4cr 2D (2.39)

where c is a proportionality constant for eq. 2.37. Equating eqs. 2.38 and 2.39 will
give
(3r 2 )D = 4r 2D (2.40)

which can be solved for the Hausdorff dimension of the Koch curve.

ln 4
D= ≈ 1.26... (2.41)
ln 3

The value of D represents the dimensionality of the object; here it is close to one,
which is somehow comforting because an infinity long curve is, in some sense, more
than a one-dimensional object without being a two dimensional area.
Coming back to polymers the Flory value ν is related with the Hausdorff dimen-
sion in the following way
1
ν≡ (2.42)
D
The Flory value of ν for a two-dimensional polymer chain in good solvent conditions,
is ν = 3/4, and its Hausdorff dimension is D = 1.333...; this is quite close to the
Hausdorff dimension for the Koch curve. However, polymers are finite random
fractals, quite different from the Koch curve which is an example of a regular fractal.
We emphasise two key differences. (a) A polymer is a self-similar object because
if its smaller sections are magnified, they look similar to the whole chain. Unlike
2.4 Fractals and self-similarity 28

regular fractals the magnified sections do not look exactly like the whole chain, but
only on average. (b) Polymers can span many length scales but remain finite. Their
self-similar features manifest themselves between the length scales of the monomer
and that of the whole chain. This comes in contrast with regular fractals which are
self-similar on all length scales.

2.4.2 Fractal universe


Mathematical fractals remain invariant to any change of scale. Polymers are not the
only objects that manifest this property. That is because the underlying concept
of fractals is symmetry – by symmetry we mean an invariance against change –
and symmetry is everywhere in Nature. For example a widely noticed symmetry
is the mirror symmetry, that is, invariance against flipping sides. Nature’s most
fundamental laws of physics, such as Newton’s law of gravitation, have an exact
mirror symmetry: there is no difference between left and right. Nevertheless the non-
conservation of parity in radioactive decay – that is the violation of point symmetry
in the weak interactions needs to be noted. Emmy Noether was the first to point out
the connection between the symmetries in the fundamental laws of physics and the
conservation of energy and momentum. In chapter 6 we observe that patterns of
two-dimensional binary mixtures of dipolar colloids remain unchanged over wide
ranges of density. The cause of this invariance in this example lies in the interactions
between the colloids, which scales with a power law ∼ 1/r 3 . As we have seen in
previous examples, power laws are related with fractals, due to their slow decaying
tail spanning many (length) scales. In chapter 5 we discuss scale-free networks which
relate and explain how physical systems that might look very different, such as
protein networks, sexual contact networks and the Internet, can be governed by the
same laws.
Chapter 3

Adsorption and self-assembly of linear


polymers on surfaces

3.1 Introduction

Polymers near to, or adsorbed on, surfaces exhibit useful and interesting proper-
ties. Adsorbed polymers find application in colloid stabilisation, [16, 17] nanoscale
surface patterning, [18] friction modification, [19, 20] DNA microarrays [21] and
adhesion. [22] Polymers can be attached to appropriate surfaces either through
chemisorption/grafting (i.e., anchoring by chemical bonds) or by physisorption (i.e.,
chain attachment by van der Waals interactions). For a weakly adsorbing surface
the physisorption and resulting conformational relaxation of the chain is driven by
the competition between the entropic repulsion due to the loss of conformational
freedom and the drop in energy from binding monomers to the substrate. Earlier
investigations have focused on thin-film polymer blends, [23, 24, 25] block copoly-
mer micelles adsorbed on surfaces, [26, 27, 28] end-grafted polymers chemisorbed
on surfaces, [29, 30, 31] and several other complex systems. The simple case of ho-
mopolymer chains physisorbed on a substrate has been studied with simulations of
free [32, 33, 34, 35, 36, 37, 38] and tethered chains, [39, 40, 41] and through theoretical
approaches; [14, 42, 43] experimental studies, however, are scarce.
In recent work by our groups, we studied the physisorption and self-assembly
of star [2] and linear [1] polymers on smooth surfaces using using atomic-force
microscopy (AFM). In a typical experiment, a polymer solution was prepared in good
solvent at concentrations below the critical overlap volume fraction (φ∗ ), resulting
in well-separated chains in solution and hence precluding any strong degree of
structural ordering within the polymer component. Polymer (sub-)monolayers were
formed by exposing a smooth surface (such as highly ordered pyrolytic graphite

29
3.1 Introduction 30

(a) (b)

Figure 3.1: (Colour online) (a) AFM image of linear polybutadiene (molecular
mass 78.8 kDa) adsorbed on mica from toluene at a surface concentration of
7.75 × 10−2 mg m−2 . The image size is 6 × 6 µm2 . (b) Cluster-height distribution
corresponding to the AFM image in (a).

or mica) to the polymer solution. The surface was then placed in a good solvent
bath for several hours and extensively rinsed with good solvent to remove any non-
adsorbed polymer. Finally, the samples were dried gently under a stream of nitrogen
and subsequently imaged in air by AFM in tapping mode to investigate the resulting
structures from this good solvent-to-bad solvent ‘quench’. Depending on the polymer
molecular weight, architecture, and concentration, very different surface structures
can be obtained. Chapter 4 is focused on the case of star polymers, where it was found
that the functionality (number of arms) and concentration of star polymers controls
a crossover between ‘polymer’ and ‘soft-colloid’ regimes, being distinguished by
characteristic cluster topologies, sizes, and surface coverages [2]. Using the same
experimental procedure, we have now studied the adsorption of linear polybutadiene
(PB) on to mica from toluene. A report of this investigation is in preparation [1], but
for the purposes of the current work, we present one key experimental observation
on which we will aim to gain insight using computer simulations. In Fig. 3.1(a)
we present an AFM image of a freshly cleaved mica exposed for 30 minutes to a
toluene PB solution (molecular weight 78.8 kg mol−1 ) leading to a surface coverage
of 7.75 × 10−2 mg m−2 . This image shows two distinct types of clusters. In Fig. 3.1(b)
we show the corresponding bimodal cluster-height distribution, with most probable
heights of 1 nm and 6 nm. In this chapter we aim to reproduce, and gain insight
on, the development of bimodal cluster distributions using Langevin dynamics
simulations of coarse-grained ‘bead-spring’ models of linear polymers.
In the experimental quenching procedure described above, the microscopic
3.1 Introduction 31

structures of the polymer solutions in contact with surfaces prior to quenching must
control the nature of polymer adsorption. Hence, the behaviour of polymers in
good-solvent conditions and near a surface is of considerable interest. In the past,
adsorption and depletion-layer effects have been the subjects of many experimental,
theoretical, and computer-simulation studies. Of particular relevance to the current
work is the seminal study by de Gennes focused on the monomer volume-fraction
profile φ(z) as a function of the perpendicular distance from the surface z [44]. De
Gennes considered a semidilute solution of chains in contact with a weakly attracting
wall, with the wall-monomer interaction of a range comparable to the monomer
size a. In the semidilute regime, the polymer volume fraction in solution φb > φ∗ ,
meaning that there are overlapping chains. Near the wall, chains are physisorbed
through a small number of monomers, leading to the formation of loops with charac-
teristic dimension D > a. Well away from the wall, the characteristic length scale is
the bulk correlation length ξb ∼ φ−3/4
b
[14], which in the semidilute regime is com-
parable to the polymer radius of gyration RG in bulk solution. Three regimes of z
can be identified: the proximal regime z ' a < D where φ(z) is dictated by the short-
range interactions with the wall; the central regime D < z < ξb in which “no other
length enters in the problem" [44] meaning that if ξ[φ(z)] ' z and ξ(z) ∼ φ(z)−3/4
then φ(z) ∼ z −4/3 ; and the distal regime z > ξb where [φ(z) − φb ]/φb ∼ exp (−z/ξb ).
The structure in the central regime is ‘self-similar’ or ‘scale-free’, because there is
no characteristic length scale (unlike in the proximal or distal regimes, which are
characterised by a and ξb , respectively). The existence of a self-similar structure
characterised by an exponent of − 43 has been confirmed experimentally by neutron
scattering [45] and by neutron reflectivity [46, 47, 48]. Results from Monte Carlo sim-
ulations of lattice polymer models are also consistent with this behaviour [49, 50, 51].
An incidental result of the current work is a demonstration that a coarse-grained,
off-lattice polymer model can reproduce this self-similar structure, and with the
correct exponent.
In this chapter we report a simulation study of adsorbed linear-polymer films.
We use Langevin dynamics simulations of coarse-grained ‘bead-spring’ models to
gain insight on the results from polymer adsorption experiments. The outline of the
study is as follows. Firstly, we study the properties of isolated adsorbed polymers
(vanishing surface coverage). This situation has been considered many times before
(see, e.g., Ref. [38]), but for the purposes of comparison with the case of finite surface
coverage, we reconsider specific single-molecule structural properties for the par-
ticular coarse-grained models being employed. Next, we deal with many polymers
on a surface under good-solvent conditions, corresponding to the prelude to the
bad-solvent quench in experiments. Of particular interest are simulation measure-
3.2 Simulation model and methods 32

ments of φ(z) and the comparison with de Gennes’ theoretical predictions. Finally,
we simulate the good solvent-to-bad solvent quench, and its effects on the structure
of the polymer film. Specifically, we identify under what conditions a bimodal cluster
distribution (such as those seen in experiments – Fig. 3.1) should be expected. The
chapter is organised as follows. Section 3.2 contains details of the coarse-grained
polymer model, and the simulation methods. Results for isolated polymers and many
polymers are presented in section 3.3. Section 3.4 concludes the chapter.

3.2 Simulation model and methods

Linear polymers are modelled as chains of N coarse-grained ‘beads’ connected


by ‘springs’. The physical motivation for such a model stems from the fact that
correlations between monomers die off beyond a characteristic length, called the
Kuhn length b. Hence, if a number of contiguous monomers are rendered by a single
bead of dimension b, then the scaling properties of the chain on length scales larger
than b will be left invariant [14, 52, 53]. Such bead-spring models of linear and star
polymers were first introduced and employed in simulations by Grest and co-workers
[54, 55, 56, 57]. In this work, N beads of equal mass m are connected to form a chain
using a non-linear finitely extensible (FENE) potential between neighbouring beads,
given by à !
1 2 r2
VFENE (r ) = − kR 0 ln 1 − 2 . (3.1)
2 R0
Here r is the bead-bead separation, R 0 is the maximum possible (bonded) bead-
bead separation, and k is a spring constant. In this study we use parameters from
earlier work [55], namely R 0 = 3σ/2 and k = 30ε/σ2 ; ε and σ are the energy and range
parameters, respectively, for the non-bonded interactions to be defined next.

The non-bonded interactions operate between all pairs of beads, and are de-
rived from a composite potential devised by Steinhauser [58]. The potential is a
combination of three terms. First we write the purely repulsive Weeks-Chandler-
Andersen (WCA) potential [59], which is a Lennard-Jones potential cut and shifted at
the position of the minimum, r min = 21/6 σ:
h¡ ¢ ¡ σ ¢6 i
σ 12
(
4ε r − r + ε r ≤ r min
VWCA (r ) = (3.2)
0 r > r min

To represent the attractive interactions, the WCA potential is shifted back down in
3.2 Simulation model and methods 33

the range 0 ≤ r ≤ r min by a square-well (SW) potential


(
−λε 0 < r ≤ r min
VSW (r ) (3.3)
0 r > r min

where λ reflects the solvent quality (to be discussed below). To interpolate the
potential smoothly between −λε at r = r min and 0 at a cut-off distance r cut > r min , we
add the term
(
1
2 λε cos (αr 2 + β) − 1 r min < r ≤ r cut
£ ¤
Vcos (r ) = (3.4)
0 r > r cut

α and β satisfy the conditions αr min


2
+ β = π and αr cut
2
+ β = 2π. The cosine form of
the potential also means that dVcos /dr = 0 at r = r cut . Following earlier work [58], we
choose r cut = 3σ/2, for which the appropriate parameters are


α = p
3
= 3.173 072 868 (3.5)
9−4 2
9
β = 2π − α = −0.856 228 645. (3.6)
4

The final, non-bonded potential is V (r ) = VWCA + VSW (r ) + Vcos (r ), and is sketched


in Fig. 3.2. The parameter λ controls the depth of the potential well at r = r min ,
and provides a convenient measure of the solvent quality. In a good solvent, the
effective bead-bead interactions are purely repulsive; this corresponds to λ = 0. In
a bad solvent, the bead-bead interactions are attractive, and this behaviour can be
modelled with λ = 1; this corresponds to an attractive well of depth ² which sets the
molecular energy. θ-solvent conditions – under which the chain statistics are very
similar to those for an ideal (non-interacting) chain – are reproduced by λ = 0.646
[58].
For simulations involving a surface, an additional effective bead-surface potential
is used, [57] based on integrating the Lennard-Jones interactions arising from a
homogeneous distribution of sites within the surface. The potential is

2πεs 2 ³ σ ´9 ³ σ ´3
· ¸
Vs (z) = − (3.7)
3 15 z z

where z is the perpendicular distance of the bead from the surface, and εs controls
the strength of the bead-surface attraction. In our simulations we define εs in terms
of basic energy parameter ε by defining the dimensionless ratio ε∗s = εs /ε. In practice,
we concentrate on the values in the range 0.4 ≤ ε∗s ≤ 1.0.
For simulating the bead-spring polymer chains, we used Langevin dynamics
3.2 Simulation model and methods 34

Figure 3.2: (Color online) The non-bonded, bead-bead interaction potential V (r )


with λ = 0.7, showing the contributions from VWCA (r ) + VSW (r ) (blue) and Vcos (r )
(red).

in which the system is coupled to a heat bath, corresponding physically to solvent.


In addition to the conservative forces arising from the interaction potentials de-
scribed above, each bead will feel random and frictional forces mimicking the solvent
surrounding the bead. Thus the equations of motion for bead i are given by

d2 r i dr i
m 2
= −∇r i V − mΓ + Wi (t ) (3.8)
dt dt

where Γ is the friction coefficient, Wi (t ) describes the Brownian forces of the solvent
P
acting on the bead, and V = i < j Vi j is the total interaction potential. Wi (t ) is
represented by Gaussian white noise satisfying the fluctuation-dissipation theorem
[9]
〈Wi (t ) · W j (t 0 )〉 = 6k B TmΓδi j δ(t − t 0 ) (3.9)

where k B is Boltzmann’s constant, and T is the temperature. The Einstein relation


leads to a diffusion constant for an isolated bead of D 0 = k B T /mΓ. Further details
are given in Ref. [54] and in chapter 2.
Simulations were performed in an L × L × H cuboidal box with periodic boundary
conditions in all three directions and the minimum-image convention applied. The
box dimension in the z direction was set to a large, but finite, value of H = 200σ, and
the surface was represented by a structureless, L ×L ×l solid slab with a thickness l no
less than the maximum range of interaction between beads. To control the surface
bead density, L took on values of 80σ through to 180σ, which were always large
3.3 Results & discussion 35

enough for polymers in their natural conformations to avoid interacting with their
own periodic images. The simulation conditions mean that the polymers are at finite
density within the simulation cell, and so there is an equilibrium state where the
polymers are adsorbed. In principle, the polymers could adsorb on either face of the
slab, but they cannot interact with each other because l is larger than the interaction
range, and H is much larger than typical polymer dimensions (as measured by the
radius of gyration, RG ); hence, the two surfaces are essentially isolated from one
another. In practice, initial configurations were prepared by placing the polymers
on one face of the slab, and all subsequent measurements were made for that one
surface. Simulated properties are reported here in reduced units defined in terms
of m, ε, and σ. The equations of motion were integrated using the velocity-Verlet
p
algorithm with a time-step δt = 0.007τ, where τ = mσ2 /ε is the basic unit of time.
In all cases, the reduced temperature k B T /ε = 1, and the reduced friction coefficient
Γτ = 1.

3.3 Results & discussion

We have studied three different situations using Langevin dynamics simulations:


(i) the behaviour of isolated polymers on surfaces with various solvent qualities
(with 0 ≤ λ ≤ 1); (ii) the behaviour of many polymers on surfaces in good-solvent
conditions (with λ = 0), corresponding to the experimental situation before the good
solvent-to-bad solvent quench; and (iii) many polymers in bad-solvent conditions
(with λ = 1) corresponding to the post-quench situation probed in AFM experiments.
We have studied three different chain lengths (N = 50, 100, and 200 beads), a range
of different surface-energy parameters ε∗s = εs /ε, and in the many-polymer cases, a
variety of surface coverages (to be defined in section 3.3.2). The number of beads in
each of the longest chains is of the same order of magnitude as the number of Kuhn
monomers in the smallest chains studied in experiments. Such coarse-grained, bead
spring models are known to reproduce faithfully the semi-quantitative properties
of polymers, and so despite the small lengths of our chains, we anticipate that the
various trends seen in our results will be of relevance to experiments on ultra-thin
polymer films after a sudden change in the solvent quality. Our choices for ε∗s are
based achieving a suitable degree of surface adsorption. We have not attempted
the difficult problem of determining this effective interaction parameter from first
principles; this would involve using atomistic representations of the surface, polymer
and solvent in order to determine the direct and solvent-mediated forces acting
between the polymer and surface.
3.3 Results & discussion 36

3.3.1 Isolated polymer

The average conformation of a polymer in dilute solution is well understood, and has
an isotropic globular shape defined by a radius of gyration RG , which scales with the
number of monomer units N like RG ∼ N ν where ν is a characteristic exponent equal
1 1 3
to 3
in a bad solvent, 2
in a θ-solvent, and 5
in a good solvent [14]. In the proximity
of a surface, the number of available polymer conformations is reduced, leading
to a decrease in entropy. Adsorption occurs when the surface-energy parameter εs
exceeds a certain critical value, εcs , signaling that the energetic contribution to the
free-energy from polymer-surface interactions becomes significant [14, 60]. The
accompanying change in polymer conformation can be interpreted as the order
parameter a type of second-order phase transition at ε∗s = εcs [14, 60]. It is useful to
define the dimensionless variable κ

κ = (εs − εcs )/εcs (3.10)

which measures the critical distance from the critical point. We also define the scaling
variable y,
y = κN φ (3.11)

where φ is a crossover exponent; this variable appears in the scaling analysis of


polymer adsorption. [44, 42] Through scaling theory, one can identify four regimes
of adsorption depending on the values of y and κ. (a) For a repulsive wall, y < 0, the
chain trivially remains away from the surface. (b) Near the critical point, y ' 0, the
chain is equally likely to be found at the surface as it is in the solution. (c) When y À 1
with N large and κ small, adsorption is nonetheless favored because the sum of the
interactions of the individual beads with the surface outweighs the entropic penalty
penalty of the chain being near the wall. This situation is called weak coupling limit.
[44] (d) For κ > 1 the monomers are strongly attracted to the surface and the chain
lies flat. This is called the strong coupling limit. [44] Cases (a)-(c) have been studied
extensively in simulations of the particular situation where each chain is tethered
to the surface by one end; [40, 41] case (d) has been studied in simulations of free
chains. [36, 37, 38] Earlier simulations using the same type of bead-surface potential
(3.7) suggest that, in reduced units, the critical surface-energy parameter εcs /ε ∼ 0.1.
[41] The values of ε∗s used in the current simulations (reported below) correspond to
the strong-coupling regime.
All isolated-polymer simulations began by placing a linear chain in good-solvent
conditions (λ = 0) close enough to the surface for adsorption to occur. Once the chain
had adsorbed, the solvent quality was adjusted by changing λ to the desired value.
3.3 Results & discussion 37

The molecule was equilibrated for around 106 δt , and then properties were measured
over a production run of 5 × 106 δt . Figures 3.3(a) and (b) shows the probability
density p(z) of finding beads at a perpendicular distance z from the surface, from
simulations of isolated polymers consisting of N = 100 beads, with various values
of ε∗s and λ. (The density profiles are reported in this form – normalized so that
R∞
0 p(z)dz = 1 – to aid comparison with later results for many polymers at finite
densities.) In all cases there is either a local minimum or a point of inflection in
p(z) at z ' 1.2σ, and the position of these features was taken as a distance-based
criterion for assessing whether a particular bead is ‘bound’ to the surface or not.
Note that from equation (3.7) the minimum bead-surface potential energy is located
p6
at z/σ = 2/5 ' 0.86; this distance corresponds to the positions of the primary peaks
in p(z).
In Fig. 3.4 we show the average bound fraction 〈Φa 〉 and the average maximum
height 〈h〉 as functions of λ for different chain lengths and surface-energy parameters
ε∗s . With N = 50, no apparently stable adsorption occurs for ε∗s < 0.6, while for the
longer chains with N = 100 and 200, adsorption occurs when ε∗s ≥ 0.4. That is
because for ε∗s = 0.4 we are close to weak coupling regime, meaning that the sum
of individual bead’s enthalpic contributions with the surface for shorter chains is
not enough keep them on the surface. The bound fraction 〈Φa 〉 is the fraction
of beads within interaction range of the surface defined using the distance-based
criterion z ≤ 1.2σ. For all ε∗s , 〈Φa 〉 remain insensitive to N . This is in agreement
with theory and simulations, since for κ > 1 the bound fraction scales Φa ∼ N 0
[61]. It also remains insensitive to solvent quality. There is though only a weak
monotonic decrease with increasing λ; this is due to the polymers bunching up to
optimize the attractive bead-bead interactions, at the cost of bead-surface contacts.
Unsurprisingly, for a given λ, increasing ε∗s leads to a greater bound fraction.
In general, the average maximum height 〈h〉 for all systems with ε∗s ≥ 0.6 shows
a very weak dependence on λ, there being only a slight hint of an increase as the
bad-solvent conditions (λ = 1) are approached; this is due to the ‘bunching up’ of the
beads, to take advantage of their mutual attractive interactions. But on the whole,
the strong bead-surface interactions keep the polymers quite flat on the surface, with
small, short-lived ‘loops’ and ‘tails’ appearing as beads lift off the surface as a result
of thermal fluctuations.
Different behavior is observed in those systems with N = 100 and 200 beads, and
ε∗s = 0.4, in which 〈h〉 clearly decreases with increasing λ. This, again, is due to the
‘bunching up’ of the polymer chain, much like an accordion being compressed. The
difference here, though, is that with such a weak bead-surface interaction parameter,
the polymers possess only a small number of contacts with the surface, leading to
3.3 Results & discussion

Figure 3.3: (Color online) The probability distribution p(z) of finding a bead at a perpendicular distance z from the surface. All results are
for chains with N = 100 beads. (a) Isolated chain with ε∗s = 0.4 and 0 ≤ λ ≤ 1. (b) Isolated chain with λ = 0 (good solvent) and 0.4 ≤ ε∗s ≤ 1.0.
(c) Isolated chain compared to many chains (with densities ρ ∗ = 0.6, 0.8, and 1.0), all with λ = 0 (good solvent) and ε∗s = 1.0.
38
3.3 Results & discussion 39

Figure 3.4: (Color online) The bound fraction 〈Φa 〉 (top) and the average maximum
height 〈h〉 (bottom) against solvent quality λ for isolated linear chains with, from
left to right, N = 50, 100, and 200 beads, and with different surface-interaction
parameters ε∗s .

the formation of large, long-lived ‘loops’ and ‘tails’ oriented perpendicular to the
surface. When λ is increased, the loops and tails contract, leading to a reduction in
the height of the polymer; but with a weak bead-surface interaction, this process
occurs without the loops flattening out and forming new contacts with the surface.

3.3.2 Many polymers – good solvent

Polymers in good solvent experience purely repulsive mutual interactions. Appro-


priate simulations with λ = 0 were initiated by preparing configurations with many
‘curled up’ polymers on a surface, and equilibrating for around 106 δt . For chains
of N = 50, 100, and 200 beads, we initially placed 200, 100, and 50 chains on the
surface, respectively, leading to the same total number of beads in each case. Follow-
ing equilibration, we performed a production run of 2.5 × 106 δt . The adsorption is
measured by the equilibrium surface bead density, defined in terms of the number of
beads Nads belonging to those chains with at least one bead-surface contact, defined
using the distance-based criterion z ≤ 1.2σ. Note that Nads is, in general, greater
than the number of beads actually bound to the surface. The reduced surface bead
density is ρ ∗ = Nads σ2 /L 2 . By placing a fixed number of chains on surfaces of various
sizes, we simulated surface densities, up to that corresponding to the critical overlap
concetration. In other words, approached the semidilute regime within the adsorbed
film. During equilibration runs near the critical overlap concetration, some of the
polymers were seen to desorb as the polymer film approached the steady state.
3.3 Results & discussion 40

Figure 3.5: (Color online) The bound fraction 〈Φa 〉 (top) and the average maximum
height 〈h〉 (bottom) against surface bead density ρ ∗ for many linear chains with,
from left to right, N = 50, 100, and 200 beads, in good solvent (λ = 0) and with
different surface-interaction parameters ε∗s . Wherever possible, the corresponding
isolated-polymer results are shown at ρ ∗ = 0.

We first consider the average bound fraction 〈Φa 〉 and maximum height 〈h〉,
presented in Fig. 3.5. Results are shown as functions of the surface bead density ρ ∗
for chains of N = 50, 100, and 200 beads with bead-surface interaction parameters
0.4 ≤ ε∗s ≤ 1.0. For comparison, points for isolated chains are shown at ρ ∗ = 0, the
effective density in this case. In all cases, 〈Φa 〉 decreases with increasing ρ ∗ . This
may be explained by the entropic penalty associated with a reduced number of
molecular conformations due to crowding; this effect becomes more pronounced as
the surface density is increased. With purely repulsive bead-bead interactions, there
is no additional energetic gain upon adsorption (above the bead-surface interaction)
to offset the growing entropic penalty. Hence, it is more favorable for the some beads
to lift off the surface to ease crowding. Some additional observations are that for a
given N and ρ ∗ , 〈Φa 〉 increases with increasing ε∗s ; and that for a given ρ ∗ and ε∗s , 〈Φa 〉
is essentially independent of N . We note that 〈Φa 〉 has been examined in experiments
on linear-polymer films [62], but these were conducted with chemisorbed molecules,
as opposed to the physisorbed molecules considered in this work. Chemisorption
reduces sorbate mobility, and hence reduces the opportunity for reorganization. In
addition, molecules can be irreversibly chemisorbed through fewer surface contacts
than those required for physisorption. Both of these effects lead to relatively low
bound fractions, as compared to the results reported here.
Examples of the structural differences between weak and strong surface param-
eter cases are illustrated in the simulation snapshots shown in Fig. 3.6. These are
3.3 Results & discussion 41

Figure 3.6: (Color online) Top views (top) and side views (bottom) from simulations
of chains with N = 100 beads in good solvent (λ = 0). The surface dimensions are
130σ × 130σ. (Left) ε∗s = 0.4, ρ ∗ = 0.39, Nads = 6600. (Right) ε∗s = 1.0, ρ ∗ = 0.59,
Nads = 10000. Figures were prepared using Pymol (http://pymol.sourceforge.net/).

from simulations of chains with N = 100 beads. With ε∗s = 0.4 and at ρ ∗ = 0.39, the
polymers form ‘loops’ and ‘tails’, orientated away from the surface; with ε∗s = 1.0 and
at ρ ∗ = 0.59, the polymers are flat on the surface, despite the high density.

Variations in the average maximum height 〈h〉, shown in Fig. 3.5, correlate with
those in 〈Φa 〉. As the bound fraction decreases, the film height increases, reflecting
the build-up of the polymer film. Scaling theory predicts that the height 〈h〉 scales
like εν/(ν−1)
s where ν is the characteristic exponent [14, 15, 63]. For polymers in good
solvent, ν = 35 and so 〈h〉 ∼ ε−3/2
s . This applies to isolated polymers, and to many poly-
mers when the surface concentration is much greater than the bulk concentration.
Since in all cases we have an effective bulk density of zero, the scaling law should
be observed. For each system showing significant adsorption under good-solvent
conditions, we fitted 〈h〉 to the function

h0
〈h〉 = ∗ 3/2
(3.12)
(εs )

and plotted the quantities 〈h〉/h 0 on a single graph, as shown in Fig. 3.7. The results
should collapse on to the curve (ε∗s )−3/2 ; they are indeed broadly consistent with
the predicted scaling. Note that the critical surface-energy parameter is expected
to be unimportant in this analysis, because we are working in the strong-coupling
3.3 Results & discussion 42

Figure 3.7: (Color online) Scaling plot of the maximum height 〈h〉 against the surface
interaction parameter ε∗s for polymers in good-solvent conditions (λ = 0). A reduced
density of ρ ∗ = 0 corresponds to isolated polymers. The theoretical prediction [14, 15,
63] is that 〈h〉 ∼ εν/(ν−1)
s , which for good-solvent conditions (ν = 35 ) gives 〈h〉 ∼ ε−3/2
s .
h 0 is the constant of proportionality from Eq. (3.12).

regime. From the fit shown in Fig. 3.7, it is clear that the critical value of ε∗s would be
small as compared to those used in the simulations. Indeed, attempts to fit critical
parameters led to values of no more than 0.1, in reduced units, but with relative
statistical uncertainties approaching 100%.
The effects of the surface-interaction parameter on the conformations of poly-
mers in good-solvent conditions can be characterized in terms of the radius of
gyration RG defined by * +
1 X N X N
RG2 = |r i − r j |2 . (3.13)
N 2 i =1 j >i

We note that RG2 can be decomposed in to components perpendicular and parallel to


a surface, but the average value defined above is sufficient for the current purposes.
Figure 3.8 shows the ratio γ = RG2 (many)/RG2 (isolated), where RG2 (many) is for many
polymers made up of N = 200 beads in good-solvent conditions and at finite density,
and RG2 (isolated) is the corresponding value for an isolated polymer on a surface
(and therefore at an effective density of ρ ∗ = 0). Results are shown for systems with
various surface-interaction parameters. For a given ε∗s , increasing the density causes
a decrease in γ, reflecting a crowding effect due to neighboring polymers. For a given
ρ ∗ , increasing ε∗s causes a flattening of the polymers, and hence an overall reduction
in the average dimensions.
3.3 Results & discussion 43

Figure 3.8: (Color online) RG2 for many polymers, divided by RG2 for an isolated
polymer, against surface bead density ρ ∗ , for polymers with N = 200 beads in good-
solvent conditions and with various surface-interaction parameters ε∗s .

The probability density p(z) for the many-polymer case is shown in Fig. 3.3(c).
Specifically, we show results for chains consisting of N = 100 beads in pure solvent,
with λ = 0, a fixed surface-interaction parameter ε∗s = 1.0, and surface bead densities
ranging from ρ ∗ = 0 (isolated chain) to ρ ∗ = 1.0. The proximal regime, identified by
de Gennes, [44] is dominated by the bead-surface interactions, and in this case covers
the range 0 ≤ z/σ ≤ 2; the two peaks can be interpreted as arising from two ordered
layers on the surface. For an isolated chain, p(z) dies off very rapidly beyond z ' 2σ.
At finite densities, p(z) dies off rapidly at large distances, roughly corresponding to
distal regime. Under the same conditions, there is an intermediate, central regime
in which p(z) should vary like z −4/3 in good-solvent conditions [14]; our simulation
results appear to be consistent with this scaling law. For the system with ρ ∗ = 1.0, the
central regime covers the range 2 ≤ z/σ ≤ 10; approximate ranges of the proximal,
central and distal regimes for this system are indicated in Fig. 3.3(c). In general, the
theoretical scaling predictions should apply to long chains and to adsorption from
semidilute solutions. The experimental [1] and simulation conditions correspond
more closely to an adsorbed film with a pure sovent; in addition, the simulated chains
are relatively short. Our results approach the expected z −4/3 scaling as the density is
increased due to the conditions near the surface are beginning to resemble those in a
film formed by adsorption from semidilute solutions. Note that this is consistence
even for strong adsoprtion, because the polymers extend to distances of the same
order the Flory radius, R F ∼ N ν , with large loops [42]. We emphasize that this study
3.3 Results & discussion 44

was not focused on observing the predicted scaling, but it is comforting that our
simulation results are at least consistent with the theoretical predictions [44, 42, 43];
coarse-grained, off-lattice models of polymers in good solvent appear to form de
Gennes’ ‘self-similar carpet’ [43].

3.3.3 Many polymers – bad solvent

The final step in the experimental polymer-adsorption procedure being considered


here, is the quench from good-solvent to bad-solvent conditions, corresponding
to rinsing with solvent and then drying in nitrogen / air. In our simulations, we
mimic this step by starting simulations from well equilibrated configurations with
λ = 0 (good solvent) and then instantaneously switching to λ = 1 (bad solvent). We
then re-equilibrate the system for 2 × 106 δt , during which time the system was seen
to reach an apparent steady state. In our experiments, the surface structures are
apparently stable for periods of at least ten days. In our simulations no restrictions
exist in the lateral directions, e.g. surface roughness, thus allowing the polymers
slowing to diffuse on the surface. In earlier simulations of polymers films on surfaces,
apparently metastable structures have been observed for periods of time that might
extend towards experimental timescales [64]. Simulations therefore provide valuable
insights on the experimental images. Nevertheless, it is easy to imagine that the true
equilibrium state –if accessible– would correspond to a single, large (hemisperical)
polymer droplet [32, 33, 34]; so the observed behavior in our simulations might
best described as metastable. This is because the diffusion rate of an adsorbed
polymer chain in bad solvent is not only lower than in good solvent, bad also inversely
proportional to the number of beads [35]. Thus, within the simulation timescale,
clusters may not diffuse sufficiently far in order to form a putative, single-droplet
equilibrium structure. In any case, the structures we observe are apparently static on
the timescales accessed in the simulations.
Figure 3.9 shows examples of equilibrated simulation configurations before (λ =
0) and after (λ = 1) the quench, for systems of polymers each made up from N = 200
beads, with surface-interaction parameters ε∗s = 0.4, and at various densities. In
good-solvent conditions, the polymers are in extended conformations, but in bad-
solvent conditions they collapse to form globular clusters to optimize the attractive
bead-bead interactions. At high density (ρ ∗ = 0.81) the quench induces extensive
clustering, resulting in a small number of large clusters. At intermediate density
(ρ ∗ = 0.49), a mixture of single chains and large clusters is in evidence, with the
single chains in the minority. At low density (ρ ∗ = 0.30) the single chains are more
numerous.
3.3 Results & discussion 45

Figure 3.9: (Color online) Top views from simulations of chains with N = 200 beads in
good-solvent conditions (λ = 0, top) and bad-solvent conditions (λ = 1, bottom), and
with surface-interaction parameter ε∗s = 0.4. (Left) ρ ∗ = 0.81, L = 80σ, Nads = 5200.
(Center) ρ ∗ = 0.49, L = 130σ, Nads = 8200. (Right) ρ ∗ = 0.30, L = 180σ, Nads = 9720.
Figures were prepared using Pymol (http://pymol.sourceforge.net/).

In Fig. 3.10 we show cluster-size histograms for systems of polymers (N = 200


beads per polymer) in bad-solvent conditions, with fixed surface bead density
ρ ∗ = 0.30, and with various surface-interaction parameters ε∗s . Two polymers were
considered clustered if any two beads on different polymers were within a distance
of 1.5σ. Histograms were accumulated from sets of five independent good solvent-
to-bad solvent simulations. With small surface-interaction parameters (ε∗s = 0.4 and
0.6) the distribution shows a monotonic decrease from the peak corresponding to
single chains; with larger parameters (ε∗s = 0.8 and 1.0), the distribution is bimodal,
with a clear delineation between one-chain or two-chain species, and larger clusters.
The bimodal distribution is to be compared qualitatively to that found in AFM ex-
periments, Fig. 3.1(b). A direct, quantitative comparison is not feasible because we
have not considered a specific, coarse-grained molecular model tailored to describe
78.8 kDa linear PB adsorbed on mica. Another factor that might influence the pattern
formation, and that has not been considered in the simulations, is polydispersity
in the lengths of the chains. Nonetheless, we suggest that the general picture, to be
sketched out below, will apply to the real, experimental situation.
3.3 Results & discussion 46

Figure 3.10: Cluster-size histograms from simulations of polymers with N = 200


beads in bad-solvent conditions (λ = 1), at a density ρ ∗ = 0.30, and with various
surface-interaction parameters. Each histogram is an average of five independent
simulations of the good solvent-to-bad solvent quenching process. In each case, the
total number of adsorbed beads (as defined in section 3.3.2) is Nads = 10000.

Clearly, the nature of the cluster-size distribution depends on both ρ ∗ and ε∗s .
From simulations of 200-bead polymers at different densities and with different
surface-interaction parameters, we constructed a ‘phase diagram’ indicating whether
the quenched configurations in bad-solvent conditions showed monotonically de-
creasing cluster-size distributions, bimodal distributions, or distributions showing
single peaks; it is shown in Fig. 3.11. In general, low ρ ∗ / low ε∗s favors a monotoni-
cally decreasing cluster distribution. Increasing ε∗s flattens out the polymers on the
surface, while increasing ρ ∗ slightly leads to more overlaps with neighboring chains;
either change leads to more pronounced clustering and a bimodal cluster distribu-
tion. At high values of ρ ∗ and ε∗s , the clustering is extensive and the cluster-size
distribution is strongly peaked (typically at around five chains per cluster).
From these results, we can picture the polymer behavior during the good solvent-
to-bad solvent quench as follows. At low density and with a low surface-interaction
parameter, the polymers are largely isolated from one another and the probability
of forming bead-bead contacts is low because of the large mean separation and the
existence of ‘loops’ and ‘tails’ extending perpendicular to the surface. The polymer
conformations are essentially the same as for an isolated polymer. During the quench,
the majority of polymers simply fold up by themselves; successively smaller propor-
tions of the molecules form dimers, trimers, etc., leading to a monotonic, rapidly
3.4 Conclusions 47

Figure 3.11: (Color online) ‘Phase diagram’ in the plane of surface density ρ ∗ and
surface-interaction parameter ε∗s for polymers with N = 200 beads in bad-solvent
conditions (λ = 1), showing the occurrences of cluster distributions which are either
monotonic decreasing with cluster size, bimodal, or single peaked.

decaying cluster distribution. At high density and with a high surface-interaction


parameter, the polymers are held flat on the surface and hence the chains form many
more contacts with their neighbors. Therefore, during the quench, polymers aggre-
gate with their neighbors and go on to form large clusters. The cluster distribution is
consequently peaked at a relatively large value. At intermediate values of the density
or the surface-interaction parameter, the polymer conformations are not significantly
different from those of isolated polymers, but there are many more opportunities
for forming contacts with neighbors. These factors favor a mixture of the extremal
processes described above, and so give rise to a bimodal cluster distribution.

3.4 Conclusions

In this work we have used Langevin dynamics simulations of a coarse-grained, bead-


spring model to gain insight on the adsorption of linear polymers on to a smooth
surface. The main experimental results we set out to understand are AFM images of
polymers physisorbed from solution on to mica surfaces during a process of rapid
solvent evaporation. We mimicked this process by switching the bead-spring model
interactions from good-solvent to bad-solvent conditions. Of particular interest was
the experimental observation of a bimodal cluster distribution. We have shown that
this feature is favored at low-to-moderate polymer concentrations, and over a broad
range of polymer-surface interaction strengths. At high concentrations, a single-
peaked distribution is observed; at low concentrations, and with weak polymer-
3.4 Conclusions 48

surface interactions, a monotonically decaying cluster distribution is obtained. The


trends observed in simulations have been rationalized in terms of the probable
numbers of contacts between polymers before quenching from good-solvent to
bad-solvent conditions.
We have measured and rationalized the trends in a variety of other properties
including the fraction of monomer units bound to the surface, the height of the
adsorbed polymer film, and the radius of gyration of an adsorbed polymer chain.
An additional, incidental result of this study is the reproduction of an algebraically
decaying density profile within the ‘central regime’, as predicted by de Gennes using
scaling arguments [44]; the simulation results are consistent with the prediction
that the monomer density as a function of the perpendicular distance from the
surface (z) decays like z −4/3 . The existence of the central regime has been confirmed
experimentally [45, 46, 47, 48] and in Monte Carlo simulations of lattice models,
[49, 50, 51] but as far as we’re aware, this has not been demonstrated before in
simulations of an off-lattice model.
Future experimental and simulation work will be focused on the adsorption
and clustering of star polymers on smooth surfaces. In addition, the kinetics of
adsorption and clustering will be explored in detail. For now, we note that two distinct
mechanisms for the self-assembly of adsorbed polymers were identified through
inspecting movies of the simulated quenching process. In the first mechanism,
weakly adsorbed chains first collapse in to individual globules, which then slowly
diffuse over the surface and coalesce. The cluster distribution then appaerently
reaches a steady state on the simulation timescale. This process was more common
with small chains (with N = 50 beads) at low concentrations. The second mechanism
involves the development of contacts between the polymers prior to quenching,
i.e., in good-solvent conditions. Upon quenching, the chains collapse in to one
another, and form more extended structures. Occasionally, we observed a chain
bridging between two others, and causing all three to collapse simultaneously. These
mechanisms were favored by longer chains (N = 200 beads) at high concentrations.
Chapter 4

Adsorption and self-assembly of star


polymers on surfaces

4.1 Introduction

Star polymers are a special case of branched polymers. They are single molecules
composed by f flexible polymer chains tethered to a core particle, where f is called
the functionality. The average conformation of a star polymer in a dilute solution is
well understood by the standard star blob model, introduced by Daoud and Cotton
[65] and further developed in the work of Birshtein et al. [66, 67]. In the Daoud-
Cotton model, the interior of the star is regarded as a succession of concentric shells
of blobs, see Fig. 4.1. For f = 1 and 2 a star resembles a linear polymer meaning
that for low functionalities, star polymer exhibit highly aspherical conformations
[68, 69]. However, as the functionality is increased, asphericity significantly drops
and the stars become spherical and “stiffer” [70, 71, 72]. A star polymer is therefore a
hybrid between polymer-like objects and colloidal particles bridging two different
domains of physics. A great of interest has been generated recently on how stars
behave in the proximity of a substrate. One such interesting example is how stars
act as depleting agents for colloidal particles, and how they can be used to control
colloidal aggregation to produce desired ordered structures [3, 4, 5]. The situation of
star polymers on flat surfaces is of particular interest not only due to the academic
insights it can provide but also for potential industrial and technological applications.
On the basis of previous theoretical [73, 74, 75] and simulation [76, 77, 78] work
on star polymers on flat surfaces one can categorise the structures as belonging to
one of two categories. In the first case the star polymers are near the adsorption
transition, in which the polymer conformation has (almost) identical statistics when
the star polymer is in the bulk, see Fig. 4.2(a). In the second category the star polymer

49
4.1 Introduction 50

Figure 4.1: (Colour) A scematic illustration of the Daoud-Cotton blob model of a star
polymer.

statistics are greatly affected by polymer’s core being tethered on the surface, see
Fig. 4.2(b). The latter has been studied both on repulsive or marginal surfaces, whose
conformations are called star-brushes and in (strong) attractive surfaces (quasi)
two-dimensional polymer conformations are created. Nevertheless, there is an
intermediate case in which adsorption of the star polymer structure is driven only
by van der Waals interactions (physisorption) on a surface as see Fig. 4.2(c). The
resulting polymer structures are expected to show bulk statistics that is intermediate
between two-dimensional to three-dimensional limiting cases. This intermediate
type of interaction has been been omitted in the literature to date.

In recent work by our groups, we studied the physisorption and self-assembly of


linear [1] and star [2] polymers on smooth surfaces using atomic-force microscopy
(AFM). In a typical experiment, a polymer solution was prepared in good-solvent
conditions at concentrations below the critical overlap volume fraction (φ∗ ), resulting
in well-separated chains in solution and hence precluding any strong degree of
structural ordering within the polymer component. Polymer (sub-)monolayers were
formed by exposing a smooth surface (such as highly ordered pyrolytic graphite
or mica) to the polymer solution. The surface was then placed in a good solvent
bath for several hours and extensively rinsed with good solvent to remove any non-
adsorbed polymer. Finally, the samples were dried gently under a stream of nitrogen
and subsequently imaged in air by AFM in tapping mode to investigate the resulting
structures from this good solvent-to-bad solvent ‘quench’. Depending on the polymer
molecular weight, architecture, and concentration, very different surface structures
4.1 Introduction 51

can be obtained.
For the case of linear polymers under certain conditions two distinct types of
cluster were found, giving rise to a bimodal cluster-height distribution. A report of
the experimental investigation is in preparation [1], and a simulation study yielding
insight on the experimental results is in Ref. [79]. Using the same experimental pro-
cedure, we have studied the adsorption of star polybutadiene (PB) on to mica from
toluene. The functionality and concentration of star polymers control a crossover
between ‘polymer’ and ‘soft-colloid’ regimes, being distinguished by characteristic
cluster topologies, sizes, and surface coverages [2]. In this work we aim to repro-
duce, and gain insight on, the transition from star-polymer to soft-colloid regimes
using Langevin dynamics simulations of coarse-grained ‘bead-spring’ models of star
polymers.
In the past, the properties of a star polymer and its crossover between ‘polymer’
and ‘soft-colloid’ regimes has been examined experimentally, theoretically, and with
computer simulations. In particular computer simulations have helped to confirm
the predictions of the Daoud-Cotton model and its scaling concepts [55, 56]. They
have also made possible to obtain the effective interactions between star polymers
and thus further coarse-grain the whole star polymer as one ultra-soft particle [80].
This technique has provided valuable insights on the properties of star polymers,
including the phase diagram [80]. Despite the numerous simulations studies of star
polymers it is still largely unknown how the star polymers behave in the proximity of
an attractive surface. Part of problem, namely, the lack of simulation studies focusing
on this problem, is that the star’s architecture poses a significant challenge for Monte
Carlo (MC), molecular dynamics (MD), and Brownian dynamics (BD) techniques.
For example, lattice Monte Carlo simulations permit only a small number of arms,
less than 20, to be studied, while continuum Monte Carlo runs into problems when
dealing with systems with strong density fluctuations [81]. On the other hand MD and
BD simulations can study the properties of many-arms star polymers, but not yield
information on the number of configuration and thus the calculation of characteristic
exponents in scaling theory.
In this chapter we report a simulation study of adsorbed star-polymer films. We
use Langevin dynamics simulations of coarse-grained ‘bead-spring’ models to gain
insight on the results from polymer adsorption experiments. The outline of the
study is as follows. Firstly, we study the properties of isolated adsorbed polymers
(vanishing surface coverage). For the purposes of comparison with the case of finite
surface coverage, we reconsider specific single-molecule structural properties for
the particular coarse-grained models being employed. Next, we deal with many
polymers on a surface under good-solvent conditions, corresponding to the prelude
4.3 Results & Discussion 52

Figure 4.2: (Colour) Scematic illustration of the different categories of polymer


adsorption; (a) near the adsorption transition; (b) center-adsorbed; (c) physisorbed.

to the bad-solvent quench in experiments. Finally, we simulate the good solvent-


to-bad solvent quench, and its effects on the structure of the polymer film. The
chapter is organized as follows. Section 4.2 contains details of the coarse-grained
polymer model, and the simulation methods. Results for isolated polymers and many
polymers are presented in section 4.3. Section 4.4 concludes the chapter.

4.2 Simulation Model & Methods

4.2.1 Simulation Model

Star polymers are composed of f flexible linear chains, which are tethered to a small
central core to form a single molecule. Accordingly, in this work the star polymers are
modelled with f polymer chains, which are attached/bonded to a core particle. Each
chain is composed by N beads of equal size and mass connected by springs. The
size of the core particle may be larger than the size of the beads especially for f > 32,
to allow for the construction of a stable molecule without any bond breaking. We
emphasise that the core size, which was kept as small as possible, is insignificant as
compared to the star’s overall structure. A star of f arms and N beads per arm will be
expressed in the following notation f /N . Further details on the model interactions
and simulation methodology can be found in section 3.2.

4.3 Results & Discussion


We have studied three different situations using Langevin dynamics simulations: (i)
the behavior of an isolated star polymer on a surface in good-solvent conditions
(λ = 0); (ii) the behaviour of an isolated star polymer on a surface in various solvent
qualities (0 < λ ≤ 1); (iii) the behavior of many star polymers on a surface in athermal
solvent conditions (i.e. λ = 0), corresponding to the experimental situation before the
bad-solvent quench; and (iv) many star polymers in bad-solvent conditions (λ = 1)
4.3 Results & Discussion 53

Figure 4.3: (Colour) Screenshots showing isolated stars 4/100, 32/100 and 128/100
from left to right on the top row, and 4/25, 32/25 and 128/25 from left to right on the
bottom row. The interaction strength of surface is ε∗s = 0.6.

corresponding to the post-quench state probed in the AFM experiments. We have


studied star polymers with eight different functionalities ( f = 2, 4, 8, 16, 32, 50, 64
and 128), and three different chain lengths (N = 25, 50 and 100), on different surfaces
having surface-energy parameters ε∗s = εs /ε = 0.4, 0.6, 0.8 and 1.0; in the case of
many-polymers, a range of surface coverages was explored.

4.3.1 Isolated star – Athermal solvent

In the proximity of a surface, the number of available possible conformations of a star


polymer is reduced, leading to a decrease in entropy. The ‘adsorption transition’ can
be said to be the point where the star polymer is (weakly) physisorbed on the surface,
but the distance of the core from the surface is such that the number of available con-
figurations is not significantly less than the number in bulk. Essentially, the structure
of the star polymer is similar to that in the bulk. Other studies have explored how the
conformation of star polymers with the cores tethered to a surface [76]. In the case of
repulsive or marginal surfaces the core particle being tethered on the surface keeps
the star polymer adsorbed despite the entropic penalties. The configuration of a star
polymer interacting with a marginal surface with a small center-surface distance,
is similar to that of a bulk star polymer with twice as many arms [82]. In the case
of strongly attractive surfaces center-adsorbed star polymers resemble (quasi) two-
dimensional polymers. However, to the best of the knowledge of the authors’ no work
has examined the case of star polymers adsorbed on attractive surfaces but without
the core been tethered on the surface. The resulting star polymer configuration is a
balance between the star’s arms attempt to minimise the energetic contribution of
4.3 Results & Discussion 54

the free-energy arising from polymer-surface interactions and minimise the entropy
penalties for the star being near the surface. Additionally, this biased preference of
monomers towards the surface breaks (alters) the isotropic nature of the star polymer.
In this work we study the surface effects on a physisorbed star polymer and how it
changes its conformation from low to high values of f . We study model parameters
corresponding to the physisorption regime, meaning that the interaction between a
bead and the surface is of order ∼ k B T ; adsorption is favoured because of the large
number of contacts between individual beads and the surface.
All isolated polymer simulations began by placing a star polymer in good-solvent
conditions (λ = 0) and close enough to the surface for adsorption to occur. The
equilibration time needed varied with different values of f , N and ε∗s . Equilibration
was complete within 2 × 105 δt for the smallest molecules and upto 8 × 106 δt for the
largest. Finally, the measured properties were averaged over a production run of
4 × 106 δt .
In Fig. 4.4 we show how the behavior of the average maximum height of the star,
〈h〉, and the average height of the core particle, 〈h core 〉, in different perspectives as a
function of the functionality. In the first perspective we plot the ratios 〈h〉/R c and
〈h core 〉/R c , where R c is the root mean square center-end distance of a star polymer
in bulk,
f
1
(ri − rcore )2 〉1/2 .
X
Rc = 〈 (4.1)
f end points i

The first ratio provides the information on how much the overall structure is affected
by the star’s interaction with the surface, while the second ratio describes the position
of the core particle and how much the star polymer has been deformed by exposing
the core particle on the surface. In both cases, both ratios increase with increasing
f and approach the values 2 and 1, respectively, corresponding to a structure of a
star on a surface which is similar to that in the bulk. Nevertheless, we make some
important observations. The first observation is for the 128/25 star with ε∗s = 0.4, 〈h〉
is slightly above 2R c . This happens because even though the star has a very similar
structure to that in the bulk being quite spherical due to the high values of f , the
few arms having monomer contacts with the surface are stretched to increase the
monomer contacts. The stretching of these arms increase the overall height of the
star polymer. The second point concerns the change in 〈h core 〉/R c in going from
the 2/25 to 4/25 star. The decrease observed is a consequence of a transition from
unbranched to branched architecture. At f = 2 the star is effectively a linear chain
and the position of the core particle can be anywhere between the surface and the
maximum height of the molecule. However, adding one or two more arms creates a
higher density of monomers around the core making it more favorable for it to be
4.3 Results & Discussion 55

Figure 4.4: (Colour) The figures at the top row show the ratio of the maximum height
of the star, 〈h〉, over the end-to-center distance of a star in the bulk, as a function of
f with a surface for various values of ε∗s . At the middle row the figures show the ratio
of the distance of star’s core particle between core particle and the surface, 〈h core 〉,
over the end-to-center distance of a star in the bulk, as a function of f with a surface
for various values of ε∗s . The figures at the bottom row show the ratio between the
height of the core particle, 〈h core 〉, over the maximum average height of the star, 〈h〉.

close to the surface and from the monomer-surface interactions. Nevertheless for
higher values of ε∗s at low f , 〈h core 〉/R c remains low and at the same level, meaning
that the core particle remains close to the surface, see Fig. 4.3 (a) and (d).
In the second perspective, we look at the ratio 〈h core 〉/〈h〉 as function of f . This
quantity describes the relation between the height of the star and the position of its
core. For low values of f the ratio 〈h core 〉/〈h〉 has values slightly less then 0.5, which
means that the core is located slightly lower than the mid-height of the molecule.
The ratio has higher values and closer to 0.5 for more attractive surfaces because
possible tails or large loops from the arms contributing to 〈h〉 diminish. Thus even
though the core particle is close to the surface - as indicated by 〈h core 〉 - the ratio
increases for more attractive surfaces.
Above a threshold value of f the ratio 〈h〉/R c increases significantly, with 〈h core 〉/R c
following the lead but at a different rate. This happens because as f is increased
the number of arms effectively saturates the region near the core of the star, where
the whole structure is essentially flat on the surface. At that point 〈h core 〉/〈h〉 signifi-
cantly drops because any new arms will find the surface too crowded and they will
4.3 Results & Discussion 56

Figure 4.5: (Colour) The figure displays the vertical (continuous line) and parallel
(dashed) components of radius of gyration, 〈RG2 〉⊥ and 〈RG2 〉∥ , for star polymers having
N = 25 in various surfaces. The black line has slope 0.41, corresponding to 〈RG2 〉 ∼
f 0.41 .

become free chains, which greatly contributes to the increase of 〈h〉, see Fig. 4.3(b)
and (e). There are two characteristic conformational features, the first one is that the
adsorbed arms form a disk lying on the surface, and the second feature is that, due
to crowding, some arms become free chains and form a small ‘fountain’, see Fig. 4.3.
At this threshold there is an increase of 〈h core 〉/R c , because the area around the core
particle becomes more crowded and that brings the core particle further away from
the surface.
At higher values of f , the ratios 〈h〉/R c , 〈h core 〉/R c continue to increase towards to
values 1 and 2 respectively. The ratio 〈h core 〉/〈h〉 reaches a minimum and continues
with an increase towards to 0.5. The star polymer essentially starts to regain its bulk
shape and features, and the effects of the surface are reduced. The star polymer star
now starts to resemble a hemispherical, [Fig. 4.3(c)] or spherical droplet [Fig. 4.3(f)].
In other words the star behaves like a soft-colloid, since it is stiff enough to resist the
‘flattening’ effects of the surface. The variation of 〈h core 〉/〈h〉 with ε∗s is in reverse of
what is observed in the ‘linear polymer’ regime. For star polymers, a reduction of the
monomer-surface interaction brings 〈h core 〉/〈h〉 closer to 0.5.
To understand further the behavior of the adsorbed star polymer, we draw atten-
tion to the radius of gyration,
* +
Nt X
Nt
1
〈RG2 〉 = 2
X
(ri − r j ) . (4.2)
N t2 i =1 j =i
4.3 Results & Discussion 57

Figure 4.6: (Colour) The figures of the top row show the ratio of radius of gyration
〈RG2 〉∥ of a star polymer on a surface with diferent ε∗s , over the radius of gyration of a
star polymer in bulk (i.e. no surface), 〈RG2 0 〉∥ = 23 〈RG2 0 〉, as a function of functionality,
f , and for the three diffrent arm lengths N = 25, 50, 100.

where N t = N f +1. It is well known that for star polymers in solution 〈RG2 〉 ∼ N 2ν f 1−ν ,
with ν being the correlation length exponent. In good solvent conditions ν = 3/5,
therefore 〈RG2 〉 ∼ N 1.18 f 0.4 . When a star is away from a surface, 〈RG2 〉 is expected to
scale in a isotropic fashion. But near a surface, we need to consider the dimensions
of the star polymer with respect to the surface. Therefore, we will resolve the vector
ri − r j , in eq. 4.2 in components perpendicular (⊥) and the parallel (∥) to the surface,
and generate the corresponding radii of gyration labelled 〈RG2 〉∥ and 〈RG2 〉⊥ , the sum
of which equals 〈RG2 〉. As seen in Fig. 4.5 for the case N = 25, the components of
〈RG2 〉 deviate significantly for low functionality and for higher values of the surface
interaction strength, ε∗s . At very high values of f , the star is “stiff” enough to maintain
the spherical shape it had away from the surface. Thus in the proximity of a surface
isotropy breaks down with the collapse of scaling with f , that is 〈RG2 〉 is no longer
∼ f 0.4 , see Fig. 4.5. The strong interaction with the surface significantly alters the
structure of a low- or mid-functionality adsorbed star.

In Fig. 4.6 we plot the ratio of the parallel component of the radius of gyration
of an isolated star on the surface over its value in the bulk, 〈RG2 〉∥ /〈RG2 0 〉∥ . The ratio
essentially describes the degree of the effects on the shape/size of the star caused
by the surface. The ratio has values higher than 1 since the polymer spreads on the
lateral directions of the surface. As seen above a low functionalities the star has a
two-dimensional conformation and for high functionalities the star polymer regains
its bulk statistics. A star polymer having a two-dimensional conformation means that
we can use the scaling arguments for two-dimensional stars that is 〈RG2 〉∥ ∼ f 1−3/4 ,
4.3 Results & Discussion 58

where we have used the value of characteristic exponent, ν = 3/4, in two dimentions.
This leads to the prediction that

〈RG2 〉∥ /〈RG2 0 〉∥ ∼ f 1−3/4 / f 1−3/5 = f −3/20 (4.3)

However, the results in Fig. 4.6 do not agree with eq. 4.3. We interpret the results
as follows. At f = 2 (equivalent of linear chain) the ratio is > 1 meaning that the
star has spread out on the surface compared with that away from the surface. As
f increases a more complex image emerges. Instead of following eq. 4.3 there is a
significant decrease of the ratio meaning for example that a 4/50 star is not affected
as much as a 2/50 star on a surface. This becomes more pronounced for stronger
surface interactions. The interpretation for this behavior is that each arm of the star
polymer behaves as a linear chain. For low values of f each arm on the surface is
well separated from the rest of the arms of the star and hence there is little or no
interaction between the arms. In other words each arm is affected by the surface in
the same way as in the isolated chain of the same length. This interpretation explains
the ratio’s values for 4/50 and 4/100 stars being at the same level with the values of
2/25 and 4/50 stars, respectively. Overall, it indicates that a star of low functionality
and with long arms on a strong attractive surface resembles a network of linear
chains, with the core particle being its hub (or contact point). However, this behavior
is expected to be a finite effect. As obeserved in Fig. 4.6 the depth of the minimum is
smaller for N = 100 than for N = 50. Hence, for longer arms the depth would become
smaller, and the behaviour would be better described by eq. 4.3. As f increases there
is an increase of 〈RG2 〉∥ /〈RG2 0 〉∥ , because the new arms start to interact and to compete
for space (crowding effect), which leads to the star stretching out more on the surface.
As seen in Fig. 4.3(a) and (d), the star resembles a two-dimensional object, thus new
arms will have more pronounced effects on the structure of the star polymer. For
high values of f the ratio descreases and approaches to 1, because the star starts to
distance itself from the surface (also see Fig. 4.4) and regains the bulk characteristics
and shape.

In Fig. 4.6 we show the average bound fraction 〈Φa 〉 as a function of f , where
the bound fraction is defined as the fraction of beads within the interaction range
of the surface defined using the distance-based criterion z ≤ 1.2σ. For details see
subsection 3.3.1. At low f the behavior of 〈Φa 〉 remains at the same level for the case
of linear chains ( f = 2), since all arms are adsorbed on the surface and essentially
each behaves like a linear chain. Having more arms, will create crowding effects and
after a certain threshold the star will have arms not being adsorbed, thus reducing
the bound fraction.
4.3 Results & Discussion 59

Figure 4.7: (Colour) Snapshots of 64/100 star polymer. The top snapshot shows
the star polymer conformation in the bulk. The mid and bottom snapshots display
the topview and sideview, respectively, conformation of the star on a surface with
ε∗s = 1.0 showing how much it has spread on the surface.

To further understand the behavior of a physisorbed star on a surface we looked


at its shape. There many ways to characterize the shape of an arbitary object; in
particular for polymers one can gain valuable insights by looking at the shapes of
random walk, for an overview conserning star polymers see Ref. [83] In this work we
will use the characterization developed by Runidick et al.[84] in which the asphericity,
A d , is defined as
Pd D 2 2
E
j >i (L i
− L j
)
Ad = (4.4)
2 2
D¡P ¢ E
d
(d − 1) L
i =1 i

where L i are the principal components of the squared radius of gyration, and d is
the number of the principal components. The quantity A d has 0 as its lower bound
4.3 Results & Discussion 60

Figure 4.8: (Colour) The figure displays the degree of asphericity, for N = 25, 50 and
100 as a function of f for different values of ε∗s . In the top row the ratio of A x y z /A ∗x y z
and in bottom row the A xz are plotted.

and it is achieved when the object has a spherical shape, and has upper bound of
1 when it is extended in one dimension (rod-like). In Fig. 4.8 we plot A x y z (three-
dimensional asphericity) of a star in the bulk and on a surface for different surface
energy interactions. It provides information on how much the surface has affected a
star’s shape. In previous studies it was found that in the bulk the asphericity drops as
∼ f −1 [83], which is in agreement with our results in the bulk. However, the results
for stars on the surface show a more complex picture. For this reason in Fig. 4.8 we
also plot the A x y , which is the two-dimensional asphericity with the beads’ positions
projected on to the surface. The quantity A x y has a weak power-law dependence that
scales with ∼ f −1.4 , which is different from that found in the bulk ∼ f −1 . Moreover,
in Fig. 4.8 we plot the asphericity in the x, z directions, A xz that is one parallel and
one perpendicular to the surface. The values of A xz provide a more clear description
of an adsorbed star measuring the degree of flatness. The results show that for high
values of ε∗s and low values of f , A xz has values near 1 meaning that the profile of the
star spans only the dimensions parallel to the surface. In other words the star lies
flat on the surface. Note that the longer the arms are, the higher the functionality
is required to start regaining its bulk shape; in the case of N = 100 the threshold is
f = 32. That is because longer arms have more monomer contacts with the surface
and with their energetic contributions the star adopts configurations with higher
4.3 Results & Discussion 61

Figure 4.9: (Colour) The figures display the density profiles of adsorbed stars of
f /100 on surfaces with ε∗s = 0.4 (top) and ε∗s = 1.0 (bottom).

entropic costs. Thus one can adjust the strength of the surface interaction and the
length of the arms of a star and convert a high f star into a (nearly) two-dimensional
object, see Fig. 4.7. A more detailed investigation of the transition of an adsorbed
star between being a two- and three-dimensional regimes is in preparation.
In Fig. 4.9 we plot the probability density p(z) of finding a bead at a perpendicular
distance z from the surface for ε∗s = 0.4 and ε∗s = 1.0 for adsorbed stars with f /100
stars. In all cases there is either a local minimum or a point of inflection in p(z) at
z ' 1.2σ, and the position of these features was taken as a distance-based criterion for
assessing whether a particular bead is ‘bound’ to the surface or not. Note that from
p
6
eq. 3.7 the minimum bead-surface potential energy is located at z/σ = 2/5 ' 0.86;
this distance corresponds to the positions of the primary peaks in p(z). The first
two peaks observed in Fig. 4.9 arise from two ordered bead layers on the surface. A
third peak is observed in the case of ε∗s = 0.4 at f = 64 and 128; it corresponds to
the position of the star’s core particle. Additionally, for z > h core the density profile
p(z) ∼ z −4/3 , which corresponds to the Daoud-Cotton picture [65], in which the bulk
interior of a star in good-solvent conditions and with suffiently long arms possesses a
region in which the monomer density profile follows a power law as a function of the
distance from the star’s center. In other words, the arms of high-functionality stars
remote from weakly attractive surfaces remain unpertubed by adsorption effects.
From the results presented here three different structures have been identified,
and we use the following terminology. The linear regime corresponds to the case
where the arms do not interact significatly with one another, and so the star polymer
4.3 Results & Discussion 62

Figure 4.10: (Colour) The figure display the different regimes of a N / f star polymer
on a surface with ε∗s = 1.0.

acts like a network of loosely-coupled linear chains. The colloidal regime applies
when the star resembles an ulta-soft colloid. The star regime is intermediate be-
tween the linear and colloidal regimes. Within the star regime, a star polymer on
a surface may only extend in the lateral directions and thus it behaves like a two
dimentional object. We identify the boundaries between the linear and star regimes
using the minimum occuring of 〈RG2 〉∥ /〈RG2 0 〉∥ in Fig. 4.6. The transition between
a two-dimensional star and three-dimensional star occurs at the point just before
〈h core 〉/〈h〉 significantly decreses, after which at least one arm is desorbed from the
surface. Finally, the boundary between the star and colloidal regimes is identified
using the minimum occuring in 〈h core 〉/〈h〉. These regimes mentioned above are
plotted in a ‘phase diagram’ as shown in Fig. 4.10.

4.3.2 Isolated star - Solvent Effects


In this section we focus on the effects of the solvent on the structure of an isolated
adsorbed star polymer. Once the star polymer had adsorbed in athermal solvent
(λ = 0) followed the following procedure described in the previous section, the
solvent quality was adjusted by changing λ to the desired value. The molecule
was equilibrated for around 2 × 106 δt , and then properties were measured over a
production run of 4 × 106 δt . Note that if a change in solvent quality was more than
0.4 = λnew −λold then intermediate equilibration cycles of 106 δt were performed after
increments of ∆λ = 0.1 until the desired value was reached. The solvent parameter
values we have explored, apart from λ = 0 corresponding to athermal solvent, are
4.3 Results & Discussion 63

Figure 4.11: (Colour) The diagrams display the behavior height an adsorbed star
polymer f /50 (top row) and its core particle (bottom row). For comparison the
quantities are presented for different monomer-surface interactions, ε∗s = 0.4 (left
column) and ε∗s = 1.0 (right column).

λ = 0.4, 0.646 (θ-solvent) [58] and 1.0.


Changing the solvent quality means that the monomer-monomer interactions
become less repulsive and the crowding effects are reduced. This has an immediate
result; the star polymer shrinks in size. In Fig. 4.11 this effect is observed by measur-
ing 〈h〉 and 〈h core 〉. Both quantities are reduced by descreasing the solvent quality.
Nevertheless, a deviation from this behavior has been observed when entering in
to the bad-solvent regime for small values of ε∗s , i.e. ε∗s = 0.4. The height of the star
polymer is getting smaller, while the height of the core particle, 〈h core 〉 is slightly
increased. This is more pronouced for higher values of f . The interpretation of this
behavior is that the monomer-monomer interactions become significant compared
to the monomer-surface interactions; the monomers adopt a more spherical config-
uration in an attempt to minimize the surface contact with the bad solvent. Adopting
a more spherical configuration pushes the position of the core particle towards the
center of the star and away from the exterior surface of the star.
In Fig.4.12 we present results for 〈RG2 〉∥ and Φa . As described above when the
solvent quality is lowered the star polymer shrinks in size. The behavior of 〈RG2 〉∥
agrees with this description for both monomer-surface interactions being considered
(ε∗s = 0.4 and 1.0). On the other hand the bound fraction differs by exhibiting the
following interesting behavior. Φa remains at the same level as the solvent quality
changes from good-to-ideal solvent conditions. A small decrease of Φa is observed
when the star polymer enters into bad-solvent conditions. For ε∗s = 1.0 the entrance
4.3 Results & Discussion 64

Figure 4.12: (Colour) The diagrams display the behavior of the 〈RG2 〉∥ of an isolated
adsorbed star polymer f /50 (top row) and its bound fraction 〈Φ〉 (bottom row). For
comparison the quantities are presented for ε∗s = 0.4 (left column) and ε∗s = 1.0 (right
column).

into bad-solvent conditions Φa has a more significant decrease than for ε∗s = 0.4.
In Fig. 4.13 we summarize the effects of the solvent on the star’s conformation.
As the solvent quality shifts from good to ideal the star structure “shrinks” in the
sense that the crowding effects are not as pronouced as in the case of athermal
solvent conditions, compare Fig. 4.13(a) and (b). The maximum height of the star
and the height of the core are both reduced. Additionally, the bound fraction remains
roughly at the same level. Nevertheless, as we shift from ideal-solvent to bad-solvent
conditions two different behaviors are observed. In the first one the star polymer
attemts to minimise its surface contact with the bad solvent with a hemishperical
or almost spherical shape (droplet). The height of the star is further reduced but
the height of the core is increased because it moves closer to the center of the star’s
spherical shape, see Fig. 4.13(c). The dominant factor behind this behavior is that
the monomer-monomer interactions become energetically more significant than the
monomer-surface interactions. If the monomer-surface interactions still dominate
the energetic contributions to the free energy then the overall shape of the star will
be similar to that shown in Fig. 4.13(d), where both the heights of the star and its core
are reduced.
Additionally, a strong monomer-surface interactio can have drastic effects on
the structure in the lateral directions. Fig. 4.14 shows a comparison between star
configurations on surfaces with ε∗s = 0.4 and ε∗s = 1.0, these differences can be ob-
served. In the case of ε∗s = 0.4 the collapsed polymer has a nearly globular shape, but
4.3 Results & Discussion 65

Figure 4.13: (Colour) Schemate illustration of the conformation changes of star


polymer on an attractive surface; (a) good solvent conditions; (b) near θ-solvent
conditions; (c) bad solvent conditions and the monomer-monomer interaction is
stronger than the monomer-surface interaction; (d) bad solvent conditions and the
monomer-monomer interaction is weaker than the monomer-surface interaction.

in the case of ε∗s = 1.0 the star has an irregular/asymmetrical shape. Nevertheless,
the latter converges to a more regular/symmetrical shape for high values of f , i.e.
f ≥ 32. This is an important observation because with strongly interacting surface
one can manipulate the shape of the star polymer in the bad solvent conditions.

4.3.3 Many adsorbed stars - Athermal solvent


In good-solvent conditions, polymers experience purely repulsive effective mutual
interactions. Appropriate simulations with λ = 0 were initiated by preparing config-
urations with many polymers on a surface, and equilibrating for around 5 × 106 δt .
Due to computational constraints we were restricted by the number of molecules,
N p = 20 000/ f N , where 20 000 is the total number of beads used in all simulations
(without counting the core particles). Increasing the number of arms, the number of
molecules decreases thus making simulations of even modest values of f computa-
tionally expensive. For this reason in this study we investigated only the following
star polymers 2/25, 4/25, 8/25 and 16/25. Following equilibration, we performed a
production run of 4 × 106 δt .
The adsorption is measured by the equilibrium surface bead density, defined in
terms of the number of beads Nads belonging to those stars with at least one bead-
surface contact, defined using the distance-based criterion z ≤ 1.2σ. Note that Nads
is, in general, greater than the number of beads actually bound to the surface. The
reduced surface bead density is ρ ∗ = Nads σ2 /L 2 . Furthermore, in the adsorbed state
we define an effective intramolecular two-dimensional density of an isolated star ρ ∗
as
N
ρ iso = (4.5)
A iso
4.3 Results & Discussion 66

Figure 4.14: (Colour) Snapshots of configurations of f /100 star polymers in bad


solvent conditions on surfaces from a top-view perspective. The top row is for ε∗s = 0.4
and the bottom row is for ε∗s = 1.0. From left to the right the columns display the
configurations of stars with 8/100, 16/100 and 32/100, respectively.

where A iso is the area covered on the surface by the adsorbed polymer, given by
A iso = π〈RG2 〉∥ , where 〈RG2 〉∥ is the parallel component of the radius of gyration of
an isolated adsorbed polymer. ρ iso can also be used to define the critical overlap
concentration between star polymers. The dilute regime corresponds to ρ ∗ ¿ ρ iso ;
in this regime the individual stars are almost independent and nearly unperturbed.
For ρ ∗ > ρ iso , the excluded volume constrains lead to interaction effects between
adsorbed star polymers. Now, we introduce the scaling variable

ρ∗
γ= (4.6)
ρ iso

in terms of which γ = 1 corresponds to the critical overlap concetration. By placing a


number of stars on surfaces of various dimensions, we simulated surface densities,
up to that corresponding to the critical overlap concetration. In other words, the sim-
ulations were perfomed at surface concetrations (within the film) approaching the
semidilute regime. During equilibration runs near the critical overlap concentration,
some of the polymers were seen to desorb as the polymer film approached the steady
state.

In Fig. 4.15 we present the behavior of 〈h〉 and 〈h core 〉 with varying surface density.
For very small surface densities the star polymers are dispersed on the surface, and so
we expect identical results with those of an isolated star polymer. Nevertheless, the
4.3 Results & Discussion 67

Figure 4.15: (Colour) The diagrams display the behavior of the average maximum
height of adsorbed stars f /25 (top row) and their core particles (bottom row). For
comparison the quantities are presented for for different monomer-surface interac-
tions, ε∗s = 0.4 (left column) and ε∗s = 1.0 (right column).

surface density critical value beyond, which the polymer conformation significantly
changes, varies with functionality and the monomer-surface interaction. Under
weak-adsorption conditions (ε∗s = 0.4) only small values of γ could be addresses due
to desorption, which reduced the number of star polymers on the surface. For the
case of linear chains ( f = 2) one expects the critical density threshold to be much
higher than for f > 2. This is confirmed for strong adsorption conditions. Under
weak adsorption conditions the chain conformation is more sensitive to changes in
density. A possible interpretation is that the adsorbed chains can overlap with other
chains without entropic restrictions by adopting configurations that contain long
tails or loops.
This effect can be seen in Fig. 4.15, which shows that the height of the core particle
is more sensitive to changes in density for lower functionality star polymers. The
rate of change of 〈h core 〉 with density for f = 2 is much higher than that for f = 4 or
8, while in the case of f = 16 the rate remain negligible. For f > 2 the values of 〈h〉
remain at the same level within the range of 0 ≤ γ < 0.2; beyond this range there is an
increase. That is because at γ ≈ 0.2 the star polymers start to feel the presence of their
neighbouring star polymers. Similar behavior is observed under strong-adsorption
conditions (ε∗s = 1.0). The difference is that the density threshold, for the star polymer
statistics to change is at γ ≈ 0.5. In the strong monomer-surface interaction case,
〈h〉 starts to increase earlier than 〈h core 〉, due to crowding monomer effects on the
surface. This situation arises by the star polymer shrinking in the lateral directions
4.3 Results & Discussion 68

Figure 4.16: (Colour) The diagrams display the behavior of the ratio of the parallel
over the vertical component of the radius of gyration, 〈RG2 〉∥ /〈RG2 〉⊥ , of adsorbed stars
f /25 (top row) and their bound fraction (bottom row). For comparison the quantities
are presented for for different monomer-surface interactions, ε∗s = 0.4 (left column)
and ε∗s = 1.0 (right column).

and then, if the crowding effects persist, some arms desorb from the surface. The
reasoning is similar to the case of isolated star of varying functionality.
In Fig. 4.16 we display the behavior of the ratio of the parallel and the perpendic-
ular components of the radius of gyration, 〈RG2 〉∥ /〈RG2 〉⊥ , and the bound fraction, Φa .
The results show that under weak-adsorption conditions small structural changes
occur with a small decrease of 〈RG2 〉∥ /〈RG2 〉⊥ by about less that 20%. Even though
γ < 0.6 meaning there is still enough space on the surface for more star polymers
to be adsorbed, the star polymers do experience small configurational changes due
to their interactions with neighbours. One interpretation for this is that the star
polymers diffuse on the surface and eventualy they will “collide” with each other.
Once such a collision occurs there would be a degree of interpenetration, which will
affect the overall conformation of both colliding stars. Additionally, the functionality
plays an important role both on the degree of interpenetration and resulting confor-
mational changes. For example, a star polymer of f = 2 will diffuse more easily on the
surface than a star of f > 2 (keeping the arm length fixed). Additionally, desorption of
one of the arms will be more significant in a star of lower functionality. This explains
why the conformation of a star f = 2 is most sensitive to density changes.
For strong adsorption more significant changes occur, because the star polymer
extend further in the lateral directions. The star polymers possess higher values of
〈RG2 〉∥ - as shown in Fig. 4.5 - and thus they are more likely to overlap with other
4.3 Results & Discussion 69

Figure 4.17: (Colour) Top view from simulations of star polymers on an attractive
surface ε∗s = 0.4 in good-solvent conditions (λ = 0, top) and bad-solvent conditions
(λ = 1.0, bottom). All stars in the figure have N = 25 and from left to right ( f , γ) =
(2, 0.107), (4, 0.186), (8, 0.466) and (16, 0.750), respectively.

star polymers. Another key difference with the weak adsorption case is that the
configuration of the star polymer will be in the linear- or 2D-star regime. The arms
will be flatter on the surface, greatly reducing the opportunities for interpenetration.
Another factor that controls the degree of interpenetration is functionality. As func-
tionality increases both the ratio 〈RG2 〉∥ /〈RG2 〉⊥ and Φa drop, as shown in Fig. 4.16.
This is no surprise since functionality controls the “stiffness” of the stars.

4.3.4 Many adsorbed stars - Bad Solvent

The final step in the experimental polymer-adsorption procedure being considered


here, is the quench from good-solvent to bad-solvent conditions, corresponding
to rinsing with solvent and then drying in nitrogen/air. As described in chapter 3
for the case of linear chains we mimic this step in our simulations by starting sim-
ulations from well-equilibrated configurations with λ = 0 (good solvent) and then
instantaneously switching to λ = 1 (bad solvent). We then re-equilibrate the system
for 5 × 106 δt , during which the system was seen to reach an apparent steady state.
As discussed in the case of linear polymers in chapter 3 the surface structures are
apparently stable for a long period of time. Star polymers diffuse less as functionality
is increased, and so in our simulations the structures observed are apparently static
on the timescales accessed in the simulations.
In Fig. 4.17 we show examples of equilibrated simulation configurations before
(λ = 0) and after (λ = 1) the quench, for systems of polymers each made up from
4.4 Conclusions 70

N = 25 beads per arm, and with surface-interaction parameter ε∗s = 0.4, with dif-
ferent functionalities, and at various surface densities. In good-solvent conditions
the polymers are in extended conformations, but in bad-solvent conditions they
collapse to optimise the attractive bead-bead interactions. Functionality plays a
significant role in determining the degree of clustering between the polymers. As
seen in Fig. 4.17 even at a low densities, a low functionalities of f = 2 or 4 leads to
clusters composed of 4 or even 6 polymers, while for f = 16 one has to reach higher
values of surface coverage (γ ≈ 0.750) to observe a cluster composed of 3 polymers.
The interpenetration of this is based on ‘stiffness’ of the star polymer before the
quench. For low functionalities the star polymers diffuse in the lateral directions
and once they ‘collide’ they easily interpenetrate with one another. Once the quench
occurs some of the polymers will overlap each other or they are very close together
meaning that is highly probable they will form clusters. However, for higher values of
f the degree of interpenetration between polymers is greatly reduced. Therefore high
functionality stars, prior the quench, position themselves in such a way to minimise
the degree of overlapping with each other. Hence, after the quench the star polymers
tend to form isolated collapsed globules or small clusters. To observe clustering of
high functionality star polymers, one has to significantly increase the surface density
resulting an increase to the degree of polymer overlap. Another important factor that
contributes is that the functionality greatly reduces the mobility (diffusion) of the
star polymers on the surface. This means that the positions of the center of mass
of the star polymers on the surface before and after the quench will be roughly the
same. Exceptions to this would occur if a star polymer has many bead contacts or
entanglements with a neighbouring star polymer prior the quench.

4.4 Conclusions

In this work we have used Langevin dynamics simulations of coarse-grained, bead-


spring models to gain insight on the adsorption of star polymers on to a smooth
surface. Our motivation was driven by experimental AFM images of polymers ph-
ysisorbed from solution on to a mica surfaces during a process of rapid solvent
evaporation. The process was mimicked by switching the coarse-grained model in-
teractions between those appropiate for good-solvent or bad-solvent conditions. Of
particular interest was the experimental observation of the crossover from polymer-
like to colloidal behavior. Initially, we examined how the crossover manifests itself in
an isolated adsorbed polymer. Three parameters were identified being important
for controling the structure of the star on the surface: f , N and ε∗s . By exploring the
4.4 Conclusions 71

parameter space we mapped the different behaviors onto a ‘phase diagram’. Addi-
tionally, our methodology allowed us to change the solvent quality by tuning one
parameter, λ, thus gaining valuable insights on the conformational behavior of the
adsorbed star in different solvent conditions. Finally, we explored systems of many
adsorbed star polymers under good-solvent conditions and the corresponding pat-
terns they create once quenched into bad-solvent conditions. The observed patterns
were rationalised in terms of the probable interpenetration between polymers before
quenching from good-solvent to bad-solvent conditions.
Chapter 5

Neighbor network in a polydisperse


hard disk fluid

5.1 Introduction

For over four decades the science of complex networks was based on results for
random graphs, obtained by Erdös and Rényi in 1959 [85]. Recent analyses reveal that
the topologies of most large, real networks deviate from those of random networks
[86]. Examples of real networks include the World Wide Web [87, 88], the Internet
[89], metabolic systems and protein-protein interactions [90, 91, 92], sexual contacts
[93], collaborations between scientists [7] and between movie actors [94], and scoring
totals of Brazilian football players [95]. The most significant deviations from random-
network behavior appear in the tail of the degree distribution p k , that is the probability
of a given vertex possessing connections to k other vertices. In random networks
p k is Poissonian, while p k for many real networks varies asymptotically like k −γ ,
where γ is a positive exponent [94]. In qualitative terms, a scale-free network is
characterized by a small number of highly-connected vertices called ‘hubs’; for a
general introduction, see Ref. [96]. Many authors identify scale-free networks as
those possessing power-law degree distributions, but as discussed fully in Ref. [97],
this is a necessary but not sufficient condition. In what follows, we will be largely
concerned with power-law degree distributions, and the term ‘scale free’ will be
employed; but it should be borne in mind that, strictly speaking, other properties are
required for the network to be termed scale free [97].
It has been suggested – but not yet confirmed – that growth and preferential
attachment are possible mechanisms by which real-world, scale-free networks can
emerge [86]; the addition of nodes to networks may capture the intrinsic evolutionary
behavior of some real-world examples. Dynamical models of the growth of cellular

72
5.1 Introduction 73

Figure 5.1: An example of an Apollonian gasket. The image was taken from Wikipedia
(http://en.wikipedia.org/wiki/Apollonian_gasket).

networks – including the effects of cell division and disappearance – can also give rise
to scale-free neighbor networks [98, 99]. Stochastic models have been proposed and
studied which can successfully reproduce certain features of real networks [94, 100],
however there are some features which cannot yet be reproduced. An example is
the assortativity of a network [101], which measures the extent to which vertices
with equal degree link with one another: in assortative networks, vertices with equal
degree are linked to one another more frequently than in a random network; in
disassortative networks, vertices with equal degree are linked to one another less
frequently than in a random network. To quote Newman, “An interesting observa-
tion is that essentially all social networks measured appear to be assortative, but
other types of networks (information networks, technological networks, biological
networks) appear to be disassortative. It is not clear what the explanation for this
result is, or even if there is any one single explanation. (Probably there is not.)" [102].
Nonetheless, it has been shown that assortativity and clustering (which means more
linked vertices share a common neighbor than would be expected by chance) can
arise if social networks are divided in to distinct groups or communities [103].
Scale-free networks are rare in real and model condensed-matter systems. One
important example is the scale-free contact network in the Apollonian packing of cir-
cles [104], in which the circle diameter distribution decays according to a power-law
with an exponent of about 1.3 [105]. The mechanical, percolation, and conductive
properties of materials possessing Apollonian-packing networks have been shown
to exhibit unusual dependences on the number of vertices [104]. In Fig. 5.1 displays
5.1 Introduction 74

an example of Apollonian disks. Such models may describe the distribution of force
in granular materials such as concrete, and networks of voids in porous media. The
percolation properties of such networks [104, 106] will clearly be of relevance to the
characteristics of certain porous media. The Apollonian packing has also been iden-
tified as a model for networks of connected minima on potential-energy surfaces of
atomic clusters [107]; the transition states (edges) between minima (vertices) exhibit
a scale-free distribution [108, 109, 110].
This chapter is concerned with the possibility of generating a simple scale-free
network in molecular simulations of a simple fluid. The model consists of poly-
disperse hard disks in two dimensions, in which the distribution of disk diameters
(σ) varies asymptotically like σ−α , where α is a positive exponent. The equilibrium
structure of the fluid phase is determined using Monte Carlo (MC) simulations, con-
ducted at constant pressure (strictly tension). Naïvely one might expect the number
of neighbors of a given disk to be proportional to the circumference and hence σ.
Due to the broad distribution of particle diameters, neighbors are identified using the
radical tessellation [111] proposed as a suitable alternative to the Voronoï construc-
tion which is usually applied to one-component systems. If the tail of the diameter
distribution follows a power law, then perhaps the neighbor distribution will vary in
a similar way. Identifying particles with vertices, and the separation vectors between
neighboring disks as edges, this situation could give rise to a scale-free neighbor net-
work, with the large particles playing the role of the hubs. In this section it is shown
that: (i) there are indications that the neighbor network in the polydisperse hard-disk
fluid possesses a power-law degree distribution, which is one of the properties of a
scale-free network; and (ii) the neighbor network is highly assortative, i.e., vertices
with equal degree are directly connected more often than in a random network. This
is an interesting situation, because the equilibrium properties of the fluid are static,
and hence dynamic mechanisms of scale-free network formation, e.g., preferential
attachment, are not applicable.
Polydisperse hard-disk fluids are of considerable intrinsic interest, for example as
models of colloidal monolayers, froths and foams, and packing and segregation in
granular materials. The packing of binary mixtures of hard disks has been studied
extensively and is shown to be highly non-trivial [112, 113, 114]; for instance, the dis-
tributions of neighbors and of cell area (as obtained from radical tessellations) show
distinct contributions arising separately from the small and large disks, indicating
the clustering of disks with equal size. Fluids with more than two components have
received far less attention, although it has been noted than in some respects the statis-
tics of the radical tesselations may conform to those of a random tesselation [112].
Specifically, it has been found that fluids of disks with a linear, decreasing diameter
5.2 Model and methods 75

distribution obey the Aboav-Weaire law, which states that the average total number of
sides of the cells (determined by tesselation) neighboring a cell with k sides increases
linearly with k [115, 116, 117]. It has been shown that the Aboav-Weaire law is a con-
sequence of a maximum-entropy (ME) principle [118, 119], the argument being that
it can be written as a linear superposition of two basic constraints, these being that
P P
k p k = 1, and for a two-dimensional tesselation k kp k = 6 (Euler); therefore, the
Aboav-Weaire law provides no new constraints and so it leads to the ME distribution.
It might therefore be anticipated that in the polydisperse hard-disk fluid considered
in this work, a maximum-entropy distribution may provide an adequate description
of the nearest-neighbor network measured in simulations.
From the viewpoint of liquid-state physics, it is interesting to construct expres-
sions for the equations of state of highly polydisperse fluids. In statistical mechanical
terms, this may stimulate progress in understanding dense, complex fluids, such as
the mixtures of macromolecules found inside living cells [120]. Therefore, a simple
equation of state is derived using scaled-particle theory (SPT) [121], and compared
with (essentially exact) results from MC simulations.
This chapter is organized as follows. Section 5.2 details the hard-disk model,
summarizes the MC and SPT approaches to be employed, and presents the derivation
of an ME estimate of p k . The results are reported and discussed in Section 5.3, and
Section 5.4 concludes the paper.

5.2 Model and methods

The model consists of N hard disks confined to a square cell of area A. The disk-
diameter distribution is given by

C
p(σ) = (5.1)
1 + (σ/σ0 )α

where σ ≥ 0, σ0 is a reference diameter, α is a positive exponent, and C is the nor-


malization constant. This particular choice of distribution was chosen so that there
is a finite number of small particles (important for the simulations), and because it
rapidly approaches the asymptotic form p(σ) ∼ σ−α . The value of α should be small
enough to give a long tail to the distribution, but large enough such that the first few
moments are well defined. The second moment is required to exist so that one can
define a packing fraction, given by η = πρ〈σ2 〉/4, where the angled brackets denote
an average over p(σ), and ρ = N /A is the number density. The second moment is
finite only for α > 3, so present work is focused on the distribution with α = 4, the
5.2 Model and methods 76

Figure 5.2: Normalized disk-diameter distribution p(σ) = C /[1 + (σ/σ0 )4 ] plotted on


a log-log scale to highlight the asymptotic σ−4 behavior.

normalization constant and first two moments of which are


p
2 2
C = , (5.2)
πσ0
σ0
〈σ〉 = p , (5.3)
2
2 2
〈σ 〉 = σ0 . (5.4)

p(σ) is plotted in Fig. 5.2 on a log-log scale to show the crossover to a power-law
decay for σ & σ0 .

5.2.1 Monte Carlo simulations

Constant-temperature, constant-pressure MC simulations of N = 104 polydisperse


hard disks were performed in a square cell with periodic conditions applied [9].
The hard-disk system is athermal and so the reduced pressure employed in the
simulations is defined as P ∗ = P σ20 /k B T , where k B is Boltzmann’s constant and T is
the temperature. Ten different simulation configurations were used, each consisting
of particles with diameters drawn randomly from p(σ). Results obtained with the
ten configurations at a given reduced pressure were averaged.
On average, one MC cycle consisted of N attempted displacements of randomly
selected disks, N A trial displacements of ln A [9], and one cluster move, the latter
implemented using Dress and Krauth’s cluster algorithm [122] with reflection rather
5.2 Model and methods 77

Figure 5.3: A scematic illustration of the cluster move algorithm. (a) Initial config-
uration. The black dot it the random pivot point; (b) the randomly chosen particle
is reflected with respect to the pivot point; (c) particles overlaping with the new
position of particle 1 are reflected; (d) the final configuration.

than rotation [123]. The cluster moves are vital for equilibration, because the dis-
placements of large disks are severely hampered by the large number of neighboring
small disks. In a few words, each cluster move begins with the selection of a random
pivot point within the simulation box. A disk is chosen at random, and is subjected
to a point reflection about the pivot. Any disks that overlap with the reflected disk are
themselves reflected, and this process is repeated until there are no more overlaps,
see Fig. 5.3. This algorithm works particularly well at low to intermediate densities,
but it fails at high densities due to all of the particles being part of the same ‘cluster’
[123]. For each state point the equilibration phase consisted of about 105 MC cycles
with N A = 1-20, depending on the pressure. Production runs consisted of a further
105 MC cycles. At intervals of 10 MC cycles, radical tessellations [111] were com-
puted and the network statistics were incremented. In the standard two-dimensional
Voronoï construction, the edges of the tessellation are perpendicular bisectors of
the lines joining the centers of neighboring disks. When neighboring disks are of
very different size, the bisectors may intersect with the larger disks. In the radical
tessellation, this problem is avoided by forming edges with the loci of points from
5.2 Model and methods 78

which the lengths of the tangents to neighboring disks are equal.

5.2.2 Scaled particle theory

The derivation of a simple equation of state from SPT [121] is now summarized. To
begin, the excess chemical potential (in units of k B T = β−1 ) of a scaled disk with
diameter λσ is given in the limit of small λ by the Widom insertion formula [124]
· Z ¸
ex 0 0 0
βµ (λσ) ≈ − ln 1 − ρ p(σ )v(λσ, σ )dσ (5.5)

where v(λσ, σ0 ) is the excluded ‘volume’ of two hard disks with diameters λσ and σ0 :

π
v(λσ, σ0 ) = (λσ + σ0 )2 . (5.6)
4

The combination of Eqs. (5.5) and (5.6) can be expanded about λ = 0 up to a linear
term. An additional λ2 term is chosen to yield the correct limit when λ → ∞; in the
case of a scaled disk with area πλ2 σ2 /4 the reversible work of expanding the particle
against the macroscopic pressure is πP λ2 σ2 /4. The result of these manipulations is
an approximation to the excess chemical potential at fixed density and temperature:

πρσ〈σ0 〉 π
βµex (λσ) ' − ln (1 − η) + λ + βP σ2 λ2 . (5.7)
2(1 − η) 4

To obtain an equation of state, appeal is made to a relation for hard particles derived
by Smith and Labík [125, 126]. Consider the quantity Y defined by the derivative
of βµex with respect to λ at λ = 1, averaged over the diameter distribution of the
inserted particle:
dβµex (σ) ¯¯
Z ¯
Y = p(σ) dσ. (5.8)
dλ ¯
λ=1

In microscopic terms, this derivative is related to the infinitesimal work of expanding


a full-sized particle against the surrounding fluid. This is given by [127]

∂v(λσ, σ0 ) ¯¯
Z ¯
0 0
Y = ρ p(σ)p(σ )g (σ, σ ) dσdσ0
∂λ ¯
λ=1
1
Z
= πρ p(σ)p(σ0 )g (σ, σ0 )σ(σ + σ0 )dσdσ0 (5.9)
2

where g (σ, σ0 ) is the partial pair correlation function for particles with diameters
σ and σ0 , at contact. The right-hand side of this equation is simply related to the
compressibility factor, Z = βP /ρ, which is easily obtained from the virial equation
5.2 Model and methods 79

[128]:
1
Z Z
Z = 1 + πρ p(σ)p(σ0 )g (σ, σ0 )(σ + σ0 )2 dσdσ0 . (5.10)
8
Comparing Eqs. (5.9) and (5.10) leads to the simple relationship

Y = 2 (Z − 1) . (5.11)

This is the two-dimensional version of a result derived by Smith and Labík in Ref. [126].
Inserting the SPT result for βµex (λσ) [Eq. (5.7)] in to Eq. (5.8) yields

2ηs
Y = + 2Z η (5.12)
(1 − η)

where the packing fraction η = πρ〈σ2 〉/4 and s = 〈σ〉2 /〈σ2 〉. Equating Eqs. (5.11) and
(5.12) furnishes the final expression for the compressibility factor:

1 + (s − 1)η
Z= . (5.13)
(1 − η)2

The expansion of Eq (5.13) to first order in ρ is

π
Z = 1+ (1 + s)〈σ2 〉ρ + . . . (5.14)
4

which yields the correct second-virial coefficient (equal to half of the average ex-
cluded volume)

1 π π
Z Z
B2 = p(σ)p(σ0 ) (σ + σ0 )2 dσdσ0 = (1 + s)〈σ2 〉. (5.15)
2 4 4

For the disk-diameter distribution in Eq. (5.1) with α = 4, s = 12 and Z = (1 − η/2)/(1 −


η)2 = 1 + 3η/2 + . . .. Note that for the monodisperse hard-disk fluid, s = 1 and the
familiar SPT result Z = 1/(1 − η)2 is recovered.

5.2.3 Degree distribution from maximum-entropy theory


We derive a simple, ME estimate of p k (σ), this being the joint probability distribution
of neighbors for a disk with given diameter σ. The overall degree distribution p k
is then obtained by integration of p k (σ). The derivation relies on there being con-
straints on the mean and mean-square number of neighbors for a disk with given
diameter. A very small disk is essentially an ideal point particle, and because such
small disks are so numerous, the neighbor network will be essentially random with
moments that will not depend sensitively on σ. (The degree distribution for Voronoï
tesselations of random sets of points in a plane – the 2D Poisson-Voronoï tesselation
5.2 Model and methods 80

– is known [129, 130].) On the other hand, a very large disk is expected to have an
average number of neighbors which scales linearly with σ. We make the following
ansatz; the average number of neighbors for a disk with diameter σ is
P
k kp k (σ)
K 1 (σ) ≡ = a 1 + b 1 f (σ) (5.16)
p(σ)
P
where we have used the fact that k p k (σ) = p(σ), and the sums are restricted to k ≥ 3
because triangles are the smallest polygons in the tesselation. a 1 and b 1 are parame-
ters, and f (σ) is a function with the properties f (0) = 0, and limσ→∞ [ f (σ)σ0 /σ] = 1.
Given the form of p(σ), an obvious choice for f (σ) is

(σ/σ0 )α+1
f (σ) = . (5.17)
1 + (σ/σ0 )α
P 2
The mean-square number of neighbors, K 2 (σ) = kk p k (σ)/p(σ) is assumed to be
such that the width of the distribution for a given σ is constant:

K 2 (σ) − K 12 (σ)
= a2 . (5.18)
K 12 (σ)

The parameters a 1 , b 1 , and a 2 are then chosen so that


Z
p(σ)K 1 (σ)dσ = 〈k〉 (5.19)
Z
p(σ)K 2 (σ)dσ = 〈k 2 〉 (5.20)

where 〈k〉 = 6 (Euler) and 〈k 2 〉 are the averages for the whole network, and 〈k 2 〉 is to
be taken from simulation. This leads to the relationships

〈k〉 − a 1
b1 = (5.21)
〈 f (σ)〉
〈k 2 〉
a2 = −1 (5.22)
a 12 + 2a 1 b 1 〈 f (σ)〉 + b 12 〈 f 2 (σ)〉

where a 1 will be retained as an adjustable parameter. The quantity K 1 (0) = a 1 should


be less than 6 because the average of K 1 (σ) over the whole diameter distribution –
including the large disks – should be precisely 6. For the present diameter distribution
p
(5.1) with α = 4, 〈 f (σ)〉 = 1/(2 2) and 〈 f 2 (σ)〉 = 21/32. We now seek an ME solution
5.3 Results 81

for p k (σ) subject to the following constraints:

X
p k (σ) = p(σ); (5.23)
k
X
kp k (σ) = p(σ)K 1 (σ); (5.24)
k
k 2 p k (σ) = p(σ)K 2 (σ).
X
(5.25)
k

P
Maximizing the entropy S = − k≥3 p k (σ) ln p k (σ) with respect to p k (σ) (with the
method of Lagrange multipliers) leads to the result

p k (σ) = exp Λ0 (σ) + Λ1 (σ)k + Λ2 (σ)k 2 .


£ ¤
(5.26)

where the Λi (σ)s are adjusted to satisfy the constraints (5.23-5.25). Finally, p k is
obtained from the relation Z
pk = p k (σ)dσ. (5.27)

5.3 Results

5.3.1 Equation of state


Reliable simulation results were obtained for pressures up to P ∗ = 2, corresponding
to a packing fraction η ' 0.45. For higher pressures the cluster moves were seen to
result in point reflections of increasingly large clusters, which ultimately precludes
effective equilibration of the system. Presumably there is no crystallization at very
high pressure. The equation of state – plotted as P ∗ versus η – for the polydisperse
hard-disk fluid is shown in Fig. 5.4. The raw data is given in Table 5.1. The SPT (5.13)
and virial-expansion (5.14) results are shown for comparison. The SPT is surprisingly
good, being accurate for packing fractions up to about 0.3.

5.3.2 Radical tessellation and degree distribution


Simulation snapshots at P ∗ = 1 are shown in Fig. 5.5; the packing fraction at this
pressure is η ' 0.36. For clarity, only a subdomain (containing 1600 particles) of a
particular configuration is shown. Three different views are displayed: (a) the actual
hard-disk configuration; (b) the radical tessellation; and (c) the Delaunay triangles
formed by the links between neighboring vertices (defined by disks that share cell
edges).
On the basis of the radical tessellations, the degree distribution p k was con-
structed, being the probability that a disk has k neighboring disks. Given that ten
5.3 Results 82

Figure 5.4: Equation of state – reduced pressure P ∗ = βP σ20 versus packing fraction
η: MC simulations (points); SPT (solid line); virial expansion with B 2 (dashed line).

configurations were simulated, each containing 104 particles, the lower limit on p k
accessible from our simulations is ∼ 10−5 . In all cases it was confirmed that the aver-
age number of links, 〈k〉, is precisely equal to six. Figure 5.6 shows p k as measured
and averaged from simulations at P ∗ = 0.01, 0.1, 0.5, 1, 1.2, and 2. Error bars on p k
represent the statistical uncertainty in the mean obtained from averaging over the
ten distinct configurations. The small-k portions of p k (k & 10) show only small
variations over the entire range of pressures simulated. At low pressures (P ∗ < 0.5) p k
shows no sign of a long tail. At such low packing fractions, the particle positions are
uncorrelated and the degree distribution resembles that of the 2D Poisson-Voronoï
tesselation [129, 130]. At pressures in the range 0.5 ≤ P ∗ ≤ 1 it was observed that the
tail of p k for k & 21 appears as a straight line on a log-log plot, indicating consistency
with the power-law decay k −γ . At higher pressures, no power-law tail is apparent over
the range of k accessible in simulations. For all pressures P ∗ ≥ 0.1, a kink is apparent
in p k at the point where p k ' 10−4 . Since the proportions of particles contributing to
p k before and after the kink appear constant, this suggests that p k is partitioned in to
‘small-particle’ and ‘large-particle’ contributions, the latter possibly corresponding
to an asymptotic scale-free regime.
Figure 5.7 shows the tails of p k as measured in simulations with pressures in the
range 0.5 ≤ P ∗ ≤ 1. The kinks at p k ' 10−4 are more clearly visible. The asymptotic
decay of p k is consistent with a power-law, but it is far from being unambiguous. It is
difficult to access larger values of k because of limitations on the number of particles
that can be simulated; this restricts the form of the diameter distribution, and in
5.3 Results

Figure 5.5: (Color online) Sub-domain (N = 1600 particles) of a simulation configuration at P ∗ = 1 and η ' 0.36: (a) the actual hard-disk
configuration; (b) the radical tessellation; and (c) the Delaunay triangles formed by the links between neighboring vertices.
83
5.3 Results 84

Figure 5.6: (Color online) Near-neighbor distribution functions, p k , at reduced


pressures in the range 0.01 ≤ P ∗ ≤ 2.

particular necessitates the regularization of the distribution at σ < σ0 . Nevertheless,


least-squares fitting of power laws to the tails of p k yields the lines shown in Fig. 5.7.
The corresponding fitting ranges and exponents (γ) are reported in Table 5.1.
It has been pointed out that the least-squares fitting procedure may give rise to
biased, and hence erroneous, results for the power-law exponent (γ) due to large
fluctuations in the tail of the distribution [131, 132]. There is an alternative fitting
scheme based on a maximum likelihood estimator (MLE), which for power-laws
yields a simple, closed-form expression for the exponent [131, 132]. We implemented
this scheme on the cumulative probability, c k = ∞ p k ∼ k −γ+1 , which serves to
P
k
reduce statistical errors. We report the resulting MLE exponents in Table 5.1; the
values are slightly smaller than, but generally consistent with, those obtained from
least-squares fitting.
Interestingly, γ is relatively insensitive to the packing fraction, being in the region
5-6; the uncertainties quoted in Table 5.1 are associated with the fitting procedure,
and so they are underestimates. Naïvely, if the number of neighbors is proportional
to the disk diameter, then one might expect p k ∼ k −4 ; in reality, γ is significantly
greater than 4. The apparent exponent γ > α can be understood by comparing the
MC simulation results with the predictions from the ME theory derived in Section
5.2.3. Figure 5.8 shows p k from simulations with P ∗ = 0.5 and P ∗ = 1, along with
plots of Eq. (5.27) computed using the best-fit parameters a 1 = 5.50 and a 1 = 5.39,
respectively, and values of 〈k 2 〉 reported in Table 5.1. The ME results are in quite
good agreement with those from simulations, although the kink at p k ∼ 10−4 is not
5.3 Results

P∗ η 〈k〉 〈k 2 〉 w γ (LS) γ (MLE) Range r


0.01 0.0078(2) 6.00 37.758(4) 0.2210 0.475(8)
0.1 0.068(1) 6.00 37.78(7) 0.2220 0.472(14)
0.3 0.171(2) 6.00 37.88(3) 0.2285 0.467(10)
0.5 0.245(3) 6.00 38.18(3) 0.2445 6.0(1) 5.7 21 ≤ k ≤ 28 0.456(9)
0.6 0.276(3) 6.00 38.33(4) 0.2525 5.8(1) 5.7 22 ≤ k ≤ 29 0.448(7)
0.7 0.302(3) 6.00 38.44(4) 0.2581 5.9(1) 5.6 23 ≤ k ≤ 31 0.441(7)
0.8 0.324(3) 6.00 38.55(5) 0.2641 5.7(1) 5.5 23 ≤ k ≤ 32 0.433(7)
0.9 0.346(3) 6.00 38.67(4) 0.2698 5.6(1) 5.4 24 ≤ k ≤ 33 0.424(7)
1 0.362(2) 6.00 38.76(4) 0.2744 5.6(1) 5.4 24 ≤ k ≤ 34 0.420(6)
1.2 0.389(2) 6.00 38.67(7) 0.2724 0.408(3)
2 0.454(6) 6.00 39.0(1) 0.2901 0.377(6)

Table 5.1: Results from MC simulations of the polydisperse hard-disk


p fluid with α = 4: packing fraction η; mean and mean-square degree,
2 2
〈k〉 and 〈k 〉; relative width of the degree distribution, w = 〈k 〉/〈k〉2 − 1; power-law exponent, γ, for the tail of p k (and the range over
which power-law behavior is observed) from least-squares fitting (LS) and a maximum likelihood estimator (MLE) [131, 132]; assortativity r .
Figures in brackets are statistical uncertainties in the last digits based on one standard deviation.
85
5.3 Results 86

Figure 5.7: (Color online) Tails of the near-neighbor distribution functions, p k , at


reduced pressures in the range 0.5 ≤ P ∗ ≤ 1. The lines are fitted power-law extrapola-
tions p k ∼ k −γ ; the least-squares exponents are reported in Table 5.1.

captured so well. But the main points are that in the region of k = 20-30, where
the simulation results are consistent with a power-law decay, the ME predictions
have apparent exponents greater than 4 (at k = 20, γ = −d ln p k /d ln k ' 5.8), and
that as k → ∞, p k approaches the anticipated k −4 behavior (at k = 100, γ ' 4.3). Of
course, this is largely a consequence of the prescription for K 1 (σ). But the agreement
between simulation and theory at moderate k suggests that, at large enough k, the
simulated network degree-distribution would follow the power law p k ∼ k −4 .

5.3.3 Assortativity

The assortativity of a network, as defined by Newman [101], reflects the tendency


of vertices with equal degrees to cluster. A convenient measure of assortativity is
clearly defined in Ref. [101], but for clarity the derivation is reproduced here. The
degree distribution of vertices attached to randomly selected edges is not equal
to p k , because high-degree vertices have more links. Instead, the distribution is
proportional to kp k , and the distribution of remaining vertices (not including that
attached to the randomly selected edge) is q k ∝ (k + 1)p k+1 . The assortativity can
then be related to the joint probability distribution function of there being j and k
remaining vertices at each end of the selected edge [100]. Denoting this function
by e j k , the following properties are to be noted: for an undirected graph e j k =
P P
e k j ; j k e j k = 1; and j e j k = q k . For networks which are neither assortative nor
5.3 Results 87

Figure 5.8: Near-neighbor distribution functions, p k , at reduced pressures of P ∗ = 0.5


(solid points and solid line) and P ∗ = 1 (open points and dotted line) from MC
simulation (points) and the ME theory (lines).

disassortative, the degrees of the vertices at the ends of the edge are uncorrelated
and so e j k = q j q k . A correlation function between degrees can therefore be defined
P
as 〈 j k〉 − 〈 j 〉〈k〉 = j k j k(e j k − q j q k ) where the angled brackets denote an average
over all edges in the graph. For the comparison of diverse graphs, it is convenient
to normalize this correlation function by its maximal value, which corresponds to
the case of a perfectly assortative network, i.e., the degrees of connected vertices are
identical. In this case e j k = q k δ j k and j k j k(e j k − q j q k ) is equal to the variance, σ2q ,
P

of k according to the distribution q k . Finally, then, the measure of assortativity is


defined as P
jk j k(e j k − q j q k )
r= (5.28)
σ2q
where r ranges from −1 for a perfectly disassortative network, through 0 for a network
with no disassortative or assortative mixing (such as a random network [85, 101])
to +1 for a perfectly assortative network. The average values of r obtained for the
hard-disk neighbor networks are reported in Table 5.1. The results indicate that the
hard-disk fluid is strongly assortative at all pressures considered. If the degree of
a disk is dictated by its diameter, then in physical terms, the results indicate that
‘small’ disks are preferentially solvated by other small ‘disks’; the ‘large’ disks – with
high degree – are more likely to be solvated by ‘small’ disks, due to the form of the
diameter distribution. Nonetheless, some weak clustering of large disks is apparent
in Fig. 5.5, particularly in 5.5(b) and 5.5(c); note the associations between different
5.4 Conclusions 88

‘sparse’ regions of the network. The physical driving force for the clustering of large
disks might be identified with a depletion interaction [133, 134, 135] mediated by
the osmotic pressure of the small disks, but of course what constitutes the boundary
between ‘large’ and ‘small’ is not well defined. r decreases slowly and monotonically
with increasing packing fraction. One possibility is that as the packing fraction is
increased, particle packing and correlations become more pronounced, and the
‘large’ disks develop links with an increasing number of neighboring ‘small’ disks,
and the assortativity decreases. This process is, of course, accompanied by a broad-
ening of the degree distribution, as illustrated in Fig. 5.6, and as quantified by the
p
relative width, w = 〈k 2 〉/〈k〉2 − 1, reported in Table 5.1. The broadening of p k , and
the resulting effects on q k , are already taken in to account in the definition of r
[Eq. (5.28)].
The assortativities of real networks vary widely. Most ‘social’ networks, such as
scientific co-authorships and movie-actor collaborations, are clearly assortative, with
r values up to about 0.4 [101]; successful individuals are often attracted to others. On
the other hand, the networks represented by the World Wide Web, the Internet, and
most significantly, many biological situations are disassortative (with r values down
to about −0.3) [101]; this property may make the network more resilient to random
attack, since the hubs (which may play crucial roles in the function of the network)
are not connected [92]. The present simulation results indicate that if scale-free
neighbor networks do exist in the polydisperse hard-disk fluid at pressures in the
range 0.5 ≤ P ∗ ≤ 1, then they are strongly assortative, with values of r comparable
to those found in social networks. It is tempting to speculate that the analogues of
groups and communities in social networks [103] are ‘clusters’ of small and large
disks in the polydisperse fluid.

5.4 Conclusions

An attempt has been made to realize a scale-free near-neighbor network in computer


simulations of a polydisperse fluid of hard disks. Each disk represents a vertex
on a graph, and the edges of the graph correspond to links between neighboring
disks as identified by a radical tessellation. Working on the naïve assumption that
the number of links is proportional to the disk diameter, an asymptotic power-
law diameter distribution was expected to give an asymptotic power-law degree
distribution. The simulation results are consistent with power-law decay – within
the limits imposed by the simulated diameter distribution – but only for a specific
range of disk densities in which particle correlations are sufficiently pronounced.
5.4 Conclusions 89

The apparent exponent of the degree distribution γ was found to depend weakly on
the disk density, and to differ from the exponent of the diameter distribution α. A
comparison with predictions from a maximum-entropy theory suggest that this decay
is not the asymptotic one, and that for sufficiently large particles (not accessible in
simulations) γ would approach α. The results therefore suggest that, in principle,
the near-neighbor network in the polydisperse hard disk fluid may be scale-free. It is
anticipated that a similar situation would obtain with different choices of α, but of
course α should be as small as possible if a sufficient number of hubs are to be found
in a network of finite size. Earlier results [112] and the form of the maximum-entropy
theory suggest that non-power-law diameter distributions will not give rise to a scale-
free neighbor network. The assortativity of the network was found to be positive over
the whole range of disk densities, reflecting a preference for links between vertices
of equal degree. In other words, ‘small’ particles are preferentially solvated by other
‘small’ particles, and ‘large’ particles show some tendency to cluster together. Finally,
some effort was directed towards analyzing the thermodynamic properties of the
fluid. No evidence for crystallization at high packing fractions was found. A simple
equation of state – derived from a scaled-particle theory – was demonstrated to be
accurate up to moderate packing fractions.
In stochastic models of networks, the position of a vertex on a graph does not
influence its degree (i.e., the number of other vertices with which it shares edges).
But in the case of hard disks at equilibrium, the degree of a disk is dictated by its
size and the sizes of its immediate neighbors, through packing constraints. The
spatial correlations in fluids, and therefore the properties of the neighbor network,
are dictated by the requirement to minimize the free energy of the system. Hence,
the apparent scale-free properties of the network are static, and do not arise from
any dynamic mechanism, such as preferential attachment. It would be interesting to
find out whether the formation of assortative, scale-free networks in other contexts
can be rationalized using equilibrium statistical mechanics.
An experimental realization of a polydisperse ‘fluid’ could actually be a gran-
ular material, with a scale-free size distribution achieved by milling and grinding.
Alternatively, by analogy with cellular networks, froths and foams produced with
an element of bubble division and disappearance may exhibit a scale-free degree
distribution [98, 99]. It should be pointed out, however, that in conventional colloidal
fluids, polydispersity is usually better described by log-normal or Γ distributions.
The physical properties of two-dimensional materials possessing scale-free networks
may be of interest, and demand further study.
Chapter 6

Crystal structures of 2D binary


mixtures of dipolar colloids in tilted
fields

6.1 Introduction

The crystallisation of colloids confined at liquid-air and liquid-liquid interfaces


has recently attracted a great deal of attention [136, 137, 138, 139, 140, 141, 142,
143, 144] due to the large number of potential applications ranging from food and
agrochemicals to petrochemicals and pharmaceuticals. Unlike particles in the bulk,
the effective interactions between colloidal particles at fluid interfaces are influenced
not only by the properties of the particles and the solvent, but also by the surface and
line tensions of the interface [143].
From various experimental realisations of binary mixtures of dipolar colloids,
two such realisations are related with this work and we briefly describe them here.
The first realisation deals with colloidal dipoles, which are roughly spherical particles
with diameters in the range 10 nm - 1 µm. For preventing irreversible aggregation
the particles are usually coated with a thin layer of non-magnetic material. Thus
the net colloid-colloid interaction is mainly dipolar, with the coatings providing a
relatively weak short-range dispersion interactions. The colloidal dipoles are sus-
pended in a pendant drop in gravity (system I), see Fig. 6.1(a). In the second, colloids
of polystyrene colloids float on an oil-water interface (system II), see Fig. 6.1(b) .
The colloids are trapped at the oil-water interface because this way they minimise
the surface between the two phases. Nevertheless, the polystyrene colloids do not
have a molecularly smooth surface and water molecules are trapped at the colloid-
oil interface. This has as a consequence the formation of water droplets or a thin

90
6.1 Introduction 91

Figure 6.1: Scematic illustration of system I and II; (a) two colloids of different size
trapped at the oil-water interface. The dipole moments P 1 and P 2 are given by the
vector sum of the dipole moments on the particle-oil interface; (b) colloidal particles
trapped at the water-air interfacein a pendant water droplet. The external magnetic
field B is applied on the colloids.

film surrounding the polystyrene colloid with dipoles. The net dipole moment of
the dipoles surrounding the colloid is non-zero, because the dipole interaction is
screened in the aqueous phase.
In both cases, one can apply an external magnetic field to induce a repulsive
colloid-colloid interaction, whose direction and strength can easily be controlled via
the external field; the dipole moments almost perfectly align along the field direction
and the magnitude of the dipole moment is proportional to the field strength. In the
conventional setup, the field is perpendicular to the interface, inducing a repulsive
interaction between the colloids, additional to the short-ranged steric repulsion
arising from the physical cores of the colloids. For large fields, the typical strength
of the repulsive dipole-dipole interaction is much larger than the thermal energy,
leading to crystallisation of the colloids. Both realisations have been extensively
studied with experiments [136, 138, 140, 139], and simulations [141, 137, 144]. As
shown in [142] at suffiecient low density the dipole-dipole interactions of system I
and II become equivalent. The pair interactions of colloids of a binary mixture (with
diameter σA or σB ), has the form of a power law

Ψi j (r ) ∼
=(z i z j )5/2 /r 3 (6.1)

where r is the distance between the centers of the two colloids, and z i , j is either 1 or
z = σB /σA < 1 if i , j = A or B. At this regime where system I and II become equivalent
the z 5/2 corresponds to the suspensibility of the supermagnetic colloids of system I.
In this work we will work in this density regime where eq. 6.1 holds.
Knowing the effective interactions between the particles one can use computer
simulations to obtain the minimum energy configuration (MEC), and thus the fa-
6.2 Simulation Methods 92

vored crystal structure at T = 0. However, it is well known that binary mixtures tend
to exhibit a broad spectrum of rather complex alloy phases [145] corresponding to
a very rough energy landscape; few optimization algorithms are able to solve such
high-dimensional and complex problems. To overcome this difficulty, genetic algo-
rithms (GAs) have been applied to the case of binary mixtures with their interactions
been described by to eq. 6.1. The results revealed a rich spectrum of exotic ordered
ground-state structures [142].
The main focus of the current work was to explore, with the use of GA, the crystal
structures emerging from a binary mixture of colloids when the external field is tilted
with respect to the normal of the interface. The tilt angle introduces an anisotropic
interaction creating new exotic crystal structures. As the field is tilted beyond a
critical angle the patterns switch over being dominated by chains aligned parallel to
the field.
The paper is organized as follows. In Sec. 6.2 we define our model and present
the simulation methods used. The results are presented and discussed in Sec. 6.3.
Finally, in Sec. 6.4 we summarise the conclusions.

6.2 Simulation Methods

6.2.1 Model

We consider a binary mixture of particles, namely type A and B, with their diameter
ratio, z = σB /σA = 0.5, unless stated otherwise. To determine the global energy
minimum of such a system, we assume that the particles arrange themselves in a
set of Bravais lattices. Specifically, we consider a two-dimensional Bravais lattice
with an N -particle unit cell, where N is the sum of particles of type A and B, that is
N = NA + NB .
The candidate structures are generated by the periodic repetition of the unit
cell, which is a parallelogram formed by the vectors a and b that substain an angle ψ
between them, as shown in Fig. 6.2(c). For convenience, but without loss of generality,
we set the particles occupying vertices of the parallelogram to be of type A, and their
positions are described by the linear combination r = l a + mb, where l and m are
integers. We introduce a coordinate system (x, y) and, choosing the x axis parallel to
the unit-cell vector a, the primitive vectors of the Bravais lattice take the form:

a = α (x, 0)
b = α cos ψ, sin ψ
¡ ¢
(6.2)
6.2 Simulation Methods 93

Figure 6.2: (a) and (b) show schematic views of two particles, with magnetic moments
m and m0 , perfectly aligned along the external magnetic field, B. (c) The geometry
of a two-dimensional Bravais lattice with one particle per unit cell, as well the basis
vector ck that characterizes the position of an additional particle.

where x is a variable determining the length of a vector, |a| = x|b|, and α is a scal-
ing variable defined by the number density as ρ = N /|a × b| = N /xα2 sin ψ. Now,
since ρ will be fixed, it allows the elimination of one parameter of our model,
α = N /xρ sin ψ. We will call the lattice just described as the primary lattice. The
p

additional particles of the unit-cell, which can be of type A or B, are placed inside the
parallelogram, and their positions are specified by the set of vectors ck = c ka a + c kb b,
where c ka,b are coefficients and k is the index of the additional particles, k = 2, ..., N .
The value k = 1 is reserved for the coordinates of the particle belonging to the first-
lattice, c1 = (0, 0).
When such a cell is repeated periodically over space, it produces N lattices, and
each of them is shifted with respect to the first-lattice by the vectors ck . Hence, the
positions of the particles on the (x, y) plane are given by the vector r + ck .
To calculate the total energy per particle, U , in a structure defined by our model,
one has to calculate the lattice sum of all unique interactions between the particles
of the unit cell; the interactions are defined in Sec. 6.2.2, but for now they will
represented by u i , j (r). For example, if we had one particle in the unit cell, in other
words we have only the primitive lattice, then the total energy per particle would be:

1X
Ui1,i = u i i (r) (6.3)
2 r6=0

where the set {r} spans a Bravais lattice, which takes the form of a lattice sum
P∞ P∞
l =−∞ m=−∞
(...) running over the integers l and m, with the exception of (l , m) =
(0, 0). Having an additional particle in the unit cell, the total energy per particle will
be the average of the sum of each particle of the unit cell interacting with all other
particles within its own sublattice, plus the additional energy between the particles
belonging to different sublattices. Therefore the total energy per particle for two
6.2 Simulation Methods 94

particle unit cell takes the form:

1³ 1 ´ 1X
U2 = Ui ,i +U j1, j + u i , j (r + c2 − c1 ) (6.4)
2 2 r

Now, with the same reasoning we write the total energy per particle for an N -particle
unit cell:
"
1 1X X
UN = u i ,i (r)
N 2 r6=0 i =A,B
#
X NX N
−1 X
+ u i , j (r + ck − ck 0 ) (6.5)
r k=1 k 0 =k+1

Hence, the parameters that characterise the structure of the lattice are N , ρ, x, ψ,
c ka , and c kb . These parameters are subject to the following constrains:

0 < x ≤ 1, 0 < ψ ≤ π/2, 0 ≤ c ka,b ≤ 1. (6.6)

Note that the representation in eq. 6.2, even with the above constraints, is not unique,
since different sets of parameters can create equivalent structures; these ambiguities
are excluded by a suitable algorithm described in Sec. 6.2.3.
In the following we characterize composition of the binary mixture by the mole
fraction of small particles, C = NB /N . The parameter ranges we explore in this work
are, ρ = 0.4, 0.6 and 0.8, C = 1/2, 2/3, 3/4, 4/5, 1/3, 1/4, and 1/5.

6.2.2 Interactions

As mentioned in the introduction, we will study colloids with dipole-dipole interac-


tions, and with an external magnetic field, B, strong enough to create crystallization.
Before we define the interactions between the particles, we define the two compo-
nents of the B, one parallel to the plane of the interface, B∥ , and the other normal to
the interface, B⊥ , see Fig. 6.2(a). For convenience, we set the B∥ to be parallel with
the x-axis and the vector a. Therefore the field is expressed as B = |B|(cos φ, 0, sin φ).
Now, based on the approach presented in Ref. [146], the dipole-dipole pair potential
at the interface in the presence of a strong magnetic field, B, is

χi χ j B2 1
Vdd (r, χi B, χ j B) = (1 − 3 cos2 φ cos2 θ) (6.7)
2 r3

where cos θ = ∆r · B∥ /(r B ∥ ), ∆r = r + ck − ck 0 is the separation vector of two particles


on the lattice, φ is the tilt angle of the magnetic field with respect to the confining
6.2 Simulation Methods 95

Figure 6.3: (Color online) Two diagrams showing the total potential of interaction at
θ = 0 between two particles of type A (top) and one A and one B type (bottom) as a
function of interparticle separation for different values of the tilt angle, φ.

plane, and χi is the susceptibility of particle i , see Fig. 6.2(a).

However, since we will work in low enough density, where the asymptotic behav-
ior for a system of dipolar colloids when the external magnetic field is perpendicular
to the interface holds and is described by eq. 6.1, then we recall the correspondence
χi χ j B2
z i5/2 ↔ χi . Using this, we eliminate the factor 2
in eq. 6.7, and thus we can
re-write the pair dipole-dipole interaction as:

1
Vdd (r, z i , z j ) = (z i z j )5/2 3
(1 − 3 cos2 φ cos2 θ) (6.8)
r

The degree of anisotropy is controlled via the tilt angle φ, as seen in Fig. 6.4, which
allows the particles to adopt less repulsive head-to-tail configuration (θ = 0). In this
p
work we will restrict the tilt angle above the threshold value arccos(1/ 3) ≈ 54.7◦ ;
below that value, the dipole interactions in the nose-to-tail configuration becomes
attractive. The values we explore are φ = 54.7◦ , 59◦ , 64◦ , 74◦ , and 84◦ . Additionally,
we generate structures at 90◦ for comparison.

At high degree of anisotropy the particles will collapse to each other due to
the absence of repulsive interactions in the x direction. For this reason the purely
repulsive Weeks-Chandler-Andersen (WCA) potential [59], which is a Lennard-Jones
potential cut and shifted at the position of the minimum, r min = 21/6 σi j , is used to
6.2 Simulation Methods 96

Figure 6.4: (Color online) The diagram shows the total potential of interaction
between two A type particles at fixed interparticle separation, r = 1.2σ A , as a function
of θ.

model the short-ranged repulsion between the physical cores of the colloids,
·³ ´ ³ σ ´6 ¸
σi j 12

+ εi j
ij
 4ε
ij r − r r ≤ r min
VWCA (r ) = (6.9)
0 r > r min

where σi j is the effective particle diameter, and εi j sets the energy scale of the short-
ranged soft core repulsion; the values of these parameters were determined by the
p
well-known Lorentz-Berthelot mixing rules [147], ²i j = ²i i ² j j , σi j = (σi i + σ j j )/2.
Joining eq. 6.8 and eq. 6.9 together, the total pair potential takes the form:

u i , j (∆r) = Vdd (∆r, z i , z j ) + VWCA (|∆r|) (6.10)

6.2.3 Genetic Algorithms

Introduction

Many interesting optimization problems, require a reasonable fast algorithm. Given a


hard optimization problem, we need to search through a space of potential solutions
by either finding, if possible, an efficient problem-specific algorithm which is approx-
imately optimal, or by using probabilistic algorithms, which despite being powerful,
do not guarantee to give the optimum solution. For small spaces, classical exhaustive
methods usually suffice; for larger spaces special artificial intelligence techniques
6.2 Simulation Methods 97

must be employed. GAs are stochastic search algorithms invented in the 1970s by
Holland to solve high dimensional and complex problems in engineering science
[148]. These methods are inspired by the Darwinian struggle for survival and employ
evolutionary processes as key elements to obtain the optimal solution to a particular
problem. However, strictly speaking, GAs do not optimize, and neither does biologi-
cal evolution [148, 149]. Evolution uses whatever material that is at its disposal to
produce above average individuals; it has no ultimate goal of “perfection”. Neverthe-
less, GAs form the basis of extremely robust optimization methods, which are able to
take the whole search space into account, and at the same time concentrate their
computing efforts on promising regions (for an overview see Ref. [150]).

Genetic Algorithms in general

We briefly summarize the basic ideas of a GA and in the subsequent section will show
how it will be applied to our specific problem.
GA represents a candidate solution as an individual, whose genes, fixed in number,
represent the variables of the given problem. The genes in an individual can take
values from a suitably chosen alphabet, such as binary, with digits 0 and 1 as its
letters. All the genes together form the chromosome as a string of digits. Individuals
are evaluated via a problem-specific fitness function in the sense that a better or
fitter individual has a higher fitness value. A large, but fixed, number of individuals
form a generation.
The initialization of the GA’s first generation is realized at random. A new gen-
eration is formed by selecting individuals to be parents from the former generation
according to their fitness values, and then generating new individuals to form the
subsequent generation. Several procedures for this mating recombination processes
have been proposed in the literature [151]. In addition, mutations are performed with
a certain probability during the mating process, a procedure necessary to avoid per-
sistent inbreeding and to allow at the same time for the reintroduction of new or lost
genetic material. At each iteration selection-recombination-mutation-evaluation
cycle, a fraction of the former generation is replaced to form the new generation.
Usually, we retain individuals with the highest fitness value, but other replacement
procedures exist. The final solution is represented by the fittest individual in the
population after many generations.

Genetic Algorithms in our problem

These general ideas behind GAs are now applied to our problem of obtaining the
optimal crystal structure of a binary mixture of colloidal particles, by using the model
6.2 Simulation Methods 98

described in sec. 6.2.1. The formalism has been used in similar problems elsewhere
in the literature [152].
We translate our model represented by the set of parameters {x, Ψ, c 1a , c 1b , ..., c N
a b
, cN },
where Ψ = ψ/(π/2), into an individual I = I (y 1 , y 2 , ..., y 2N ), where y 1 , .., y 2N repre-
sent the parameters of our model as strings of genes of fixed length, n gene = 6. The
genes are expressed by a decimal alphabet i.e. an alphabet composed by the one-digit
integers 0, 1, 2...9. The aim of the encoding is to produce a chromosome from which
the GA will use later. For example, assuming an individual is a point in (x, y) space;
the encoding process would produce

(x, y) = (0.122334, 0.988776) → 122334988776 (6.11)

For the present investigation, we used the number of individuals, N p = 500, and the
number of generations NG = 300. Even though for most cases explored a smaller
genetic population would be suffient to give a solution; a large population maintains
diversity between individuals, and thus covering the whole search space.
As mentioned in Sec. 6.2.1, we need to implement an algorithm to ensure a unique
representation of the Bravais lattice. This is achieved by requiring the perimeter of
the unit cell, Π, to be minimal, and it is given by the equation,

Π = 2 (|a| + |b|) (6.12)

To minimize eq. 6.12, the following iterative algorithm was applied: the vectors a and
b are replaced by new vectors, from the four options the combination with the lowest
value out of Π,
{a ± b, b} and {a, a ± b} (6.13)

If none of the possible combinations minimize Π, then the algorithm stops and
the initial a and b are used. The vectors ck are not required to be checked by the
algorithm, since they are linear combination of a and b.
A positive fitness value is assigned to each individual I via the fitness function
f (I ): a higher fitness value characterizes a better solution. The optimum solution is
a crystal structure with the lowest free energy, F = U − T S, where S is entropy, but for
our purposes we look for crystals formed by the system at zero temperature (T = 0).
Therefore, the optimum crystal structure will have lowest potential energy, U , which
can be calculated by eq. 6.5 and eq. 6.10. Additionally, for practical reasons we look
at the ratio U (I )/U (I hex ), where U (I hex ) is the potential energy of a hexagonal
structure (hex) generated by one particle unit cell at the same density. The reason
behind this is to ensure that the values used will be of order 1. Hence, f (I ), in our
6.2 Simulation Methods 99

problem, reads
U (I )
½ ¾
f (I ) = exp 1 − (6.14)
U (I hex )
Once the first generation, G0 is realized and its individuals are evaluated by the
fitting function, we sort them out by a ranking scheme. For example, the fittest
£ ¤ £ ¤
individual will have rank value R f (I j ) = 1, while the least fit will have R f (I j ) =
N p . This ranking scheme is important for avoiding breeding shortcomings and to
ensure the existence of selection pressure throughout the simulation [151].
Afterwards, the interactive process of creating a new generation, starts. In the
first step, two individuals are selected as parents according to the rank of their fitness
values with the roulette wheel algorithm [151]. First, we generate a random number
w ∈ [0, S], where S is the sum of the differential fitness, S j , over all the individuals in
the population:
Np Np
£ ¤
X X N p − R f (I j ) + 1
S= Sj = (6.15)
j =1 j =1 Np

Now we use w to locate the element T j in the following inequality,

T j −1 ≤ w < T j (6.16)

where T j is the running sum,

j
X
Tj = S j , j = 1, ..., N p (6.17)
i =1

This procedure is equivalent to constructing a roulette wheel, where each individual


1
is occupying a sector of angular size S /S
2π j
and the random number represents the
spinning wheel. In other words, the probability of the wheel stopping at a sector
is proportional to the sector. Once the parents are chosen, two new individuals
populate the new generation via a one-point crossover, as visualized in Fig. 6.5.
The crossover point, which is randomly chosen, is where each of the parent’s gene
sequence is cut and combined to create the new individuals. This action is unbiased
in respect to the geometry of the problem and cannot be associated with any physical
movement of the particles. Further, we perform mutations with a probability p m ,
which has a typical value of 0.1, on the new individuals. It means that we randomly
choose one of the genes and replace it with a new one.
Even though the process of recombination and mutation will create two new
individuals, it is not guaranteed that they will join the new generation. A number of
criteria must be fulfilled. First, they must be at least as fit as the least-fit members
of the existing population; the latter will be eliminated and replaced by the new
6.3 Results & Discussion 100

Figure 6.5: (Color online) Schematic representation of the one-point crossover that
generates two new individuals from two parents.

members. Second, the new individuals must not be identical with any other member
of the population; this no-duplicate criterion is an important safeguard against
inbreeding.
To test the efficiency of the reproduction strategy described above, it was com-
pared to an alternative reproduction strategy in which we select parents randomly
with no regard to fitness, and then randomly replace members of the population with
the new individuals. An exception to this replacement is granded to the fittest indi-
vidual, as a form of elitism. Similar strategies to this has been found advantageous
for problems tending to suffer from premature convergence [153].
After the GA has provided with a solution a final optimization with gradient
descent was applied. The last step was needed to increase the accuracy of the results.

6.3 Results & Discussion


We present the ordered equilibrium configurations obtained by the GA, as the angle
of the magnetic field is tilted. The results are organizing into four blocks. (a) In
Fig. 6.6 structures with C ≥ 1/2 are shown. (b) Structures with C < 1/2 are in Fig. 6.8.
(c) A comparison with structures of different densities are in Fig. 6.9. (d) Structures
with smaller diameter ratio z = 0.3296, at ρ = 0.6 are presented in Fig. 6.10.

6.3.1 C ≥ 1/2

We start with the case C ≥ 1/2, where the small particles form more complex struc-
tures, as seen in Fig. 6.6. For the angle range 74◦ < φ < 90◦ , the patterns of the
structures only slightly perturbed from the structures at φ = 90◦ . For φ < 74◦ the
anisotropy becomes significant, and both the small and big particles attempt to take
advantage of it by generating new patterns; see Fig. 6.6(i), (m), (n), (r) and (s). At
90◦ 74◦ 64◦ 59◦ 54.7◦

C = 1/2

(a) (b) (c) (d) (e)


6.3 Results & Discussion

C = 2/3

(f) (g) (h) (i) (j)

C = 3/4

(k) (l) (m) (n) (o)

C = 4/5

(p) (q) (r) (s) (t)

Figure 6.6: (Color online) Minimum energy configurations for C ≥ 1/2, for ρ = 0.6.
101
6.3 Results & Discussion 102

Figure 6.7: (Color online) The diagram shows relative change of length of the vector
a = αx for different tilt angles.

φ = 54.7◦ there is no repulsion along the x-axis and the particles form chains parallel
to the field.
To understand the results, we view the length of vector |a| as a function of ∆φ =
90 − φ, so at ∆φ = 0◦ , |a| = |a|0 . Naively, one would expect the length of vector a to

be monotonically decrease as ∆φ increases, however that is not always the case. In


Fig. 6.7, we plot the ratio of relative displacement of the A-type particles of the first
lattice along the x-axis, (|a|0 −|a|∆φ /|a|0 ), versus ∆φ. For all cases, the ratio remains at
the same level up to the threshold ∆φ ≈ 16◦ , above that threshold it rapidly increases.
However, in the case C = 3/4, initially there is an increase, at ∆φ there is descrease,
meaning that the length of the a vector increases, but after a certain value of ∆φ,
the ratio increases as expected. Note that in our initial assumptions of our model,
the length of vector a is always smaller than the length of b. Even though, this
significantly simplifies the problem it has also the effect to limit the search space.
Nevertheless, when the restriction was removed, there was no change in our results.
An explanation for this behavior is that the small particles in the unit cell feel first
the anisotropy and attempt to come in between the primary lattice’s particles into a
head-tail configuration, compare Figs. 6.6(l) and (m). Additionally, the particles of
the primary lattice also attempt to position themselves into a more favorable oblique
formation.
Now, as the angle of the magnetic field is tilted further the particles of the primary
lattice prefer to come closer together, while increasing their separation distance in
the y-axis, as seen clearly in the cases C = 1/2 and C = 2/3, Fig. 6.6(d) and (i). In
6.3 Results & Discussion 103

the cases C = 3/4 and C = 4/5 at 59◦ , we observe that one of the small particles has
moved between the particles of the primary lattice, by creating an inhomogeneous
chain, Fig. 6.6(n) and (s). The structures at φ = 54.7◦ converge into a series of chains
parallel to the magnetic field. The small particles can form chains of uneven numbers,
Fig. 6.6(o). The reason is that the primary lattice particles come as close as possible
with each other along the x-axis, thus maximizing their distance in y-axis, and by
doing that in essence they reduce the available space for the small particles to create
chains. As the number of small particles increases there is no enough space to
accompany the third particle, therefore it creates a new chain. For C = 4/5 two such
chains composed by small particles are formed. Even though chains can be formed
for φ > 54.7◦ , such in the cases Figs. 6.6(n) and (s), some of them have mixed type of
particles something that it is not observed at φ = 54.7◦ , see Figs. 6.6(e), (j), (o) and (t).

6.3.2 C < 1/2

In the second block of results, C < 1/2, the big particles become the majority com-
ponent and attempt to form hexagonal structures, which are disturbed by the small
particle, as seen in Figs. 6.8(a), (f ) and (k). In particular, at perpendicular field,
φ = 90◦ , the neighbors of the small particle form a square, which is also seen as the
optimum structure for the system C = 1/2, see Fig. 6.6(a). Similar with the cases of
C ≥ 1/2, as the field is tilted the particles will rearrange by taking advantage of the
anisotropy.
When anisotropy becomes significant enough, the particles attempt to form
chains as seen in Figs.6.8(c), (d), (h), (i) and (m), (n). In the cases of C = 1/3 and
C = 1/5 the chains are straight, but in other case, C = 1/4, the particles’ excluded
volume comes into effect and restricts them to form straight lines. The result is to
form small zig-zags [frustrated chains], but this effect disappears as the repulsion
along the x-axis is reduced. Also, in the case of C = 1/5 see Figs.6.8(k-o), there
was no significant changes in the system’s structure due to the domination of the
big particles. The hexagonal structures change to obligue and then to chain-like
oblique structures, while the rectangular structures, created by the effects of the
small particles, do show any significant changes.
At φ = 54.7◦ the particles form chains of the same type, aligned parallel to the
field. It is interesting to note that parallel chains of particles of A-type form chain-like
oblique structures as it has been found for one component systems in Ref. [146], but
if between the chains there is a small particle, then the chains of A-type particles form
rectangular structures with be the small particle in the middle (compare Figs.6.8(e),
(j), and (o) with Fig.6.6(e)).
90◦ 74◦ 64◦ 59◦ 54.7◦

C = 1/3
6.3 Results & Discussion

(a) (b) (c) (d) (e)

C = 1/4

(f) (g) (h) (i) (j)

C = 1/5

(k) (l) (m) (n) (o)

Figure 6.8: (Color online) Minimum energy configurations for C < 1/2, for ρ = 0.6. The particles with color blue belong to the primary
lattice, while the particles with color red are A-type particles.
104
6.3 Results & Discussion 105

C = 1/2 C = 2/3 C = 4/5 C = 1/3


φ = 64◦ φ = 64◦ φ = 54.7◦ φ = 64◦

ρ = 0.8

(a) (b) (c) (d)

ρ = 0.6

(e) (f ) (g) (h)

ρ = 0.4

(i) (j) (k) (l)

Figure 6.9: (Color online) Minimum energy configuration of different compositions


as their patterns are affected by density.

6.3.3 Density effects

In sufficiently dilute concentrations of binary magnetic colloidal mixtures, the pair


potential scales as a power law at long distances, ∼ r −3 . This feature generates pat-
terns that are scale-free, meaning that the overall density is an irrelevant parameter,
as shown in previous investigations, where the field was perpendicular to the inter-
face [142]. Only at higher densities, does the excluded volume becomes a significant
factor, the system cease to be scale-free. In our simulations, we do observe the same
patterns for different values of densities for tilted external fields with non-zero in-
teraction along the x-axis. In Fig. 6.9 we present different compositions at different
densities with a tilted field, and discuss how it is affected by anisotropy. In the first
example, see Fig. 6.9(a), (f ), and (k), the system, which is at tilt angle is φ = 64◦ ,
remains invariant under change of density. In the second example, we have one more
small particle, i.e. for C = 2/3, at the same tilt angle, the system changes slightly over
different values of density, but maintain essentially the same pattern, Fig. 6.9(b), (f )
and (j). The reason is that at high density, the excluded volume becomes significant
and reduces the space between the particles. Therefore, the small particles are unable
to maintain their pattern they had at lower densities in order to take advantage of
the anisotropy.
6.4 Conclusions 106

In the first two examples, anisotropy does not affect the system’s scale-free fea-
tures. However, this is true so long there is a repulsive interaction among the particles
along the x-axis. At φ = 54.7◦ there is no interaction anymore between the particles
in the x-direction, which breaks the scale-free feature. As seen at Fig. 6.9(c), (g) and
(k), the pattern may essentially remain the same, but along the x-axis the particles
ceases to scale by not changing positions as density changes.
A final example is displayed at Fig. 6.9(d), (h) and (l), where the composition of
the system C = 1/3, which has higher packing fraction than C = 2/3, compare with
Fig. 6.9(b), (f) and (j). The anisotropy, similar to the case C = 2/3, does not affect the
system being scale-fee, till the point there is no interaction in one direction, as it
happens for φ = 54.7◦ .

6.3.4 Diameter ratio effects


In the final block of results, we look at structure with composition C > 1/2, but
with smaller diameter ratio, z = 0.3296. From a quick look at the structures, the
same behavior is observed when z = 0.5; initially the structures are perturbed, then
new structures emerge, and at φ = 54.7◦ chains are formed. Despite the similarities
there are some small but significant differences. The first one occurs for C = 2/3
at φ = 54.7◦ , Fig. 6.10(e) where the small particles form a chain, but they are not
equally spaced; the small particles form pairs. The reason behind this is that the
small particles attempt to maximize their distance from the big particles not only
along the y-axis but also the x-axis due to the absence of interactions between the
particles along the x-axis. This effect is not observed for z = 0.5, because two small
particles to cover the distance between two particles of the primary lattice.
A smaller diameter ratio also has an effect of reducing the number of chains
formed by the small particles at φ = 54.7◦ . For example, comparing C = 3/4 at z = 0.5
(Fig. 6.6(o)) and at z = 0.3296 (Fig. 6.10(j)), we observe that at lower diameter ratio
there is one less chain. As mentioned above this happens because more particles can
fit into one chain without steric repulsive iteractions come into effect.

6.4 Conclusions
We have applied genetic algorithms to study equilibrium configurations of binary
mixture of two dimensional dipolar particles in the presence of a tilted external mag-
netic field, which introduces anisotropic interactions between the particles. At small
degree of anisotropy the structures are perturbed, while once the anisotropy reaches
the maximum degree, that is when there is no repulsive (or attractive) interactions
90◦ 74◦ 64◦ 59◦ 54.7◦

C = 2/3
6.4 Conclusions

(a) (b) (c) (d) (e)

C = 3/4

(f ) (g) (h) (i) (j)

C = 4/5

(k) (l) (m) (n) (o)

C = 5/6

(p) (q) (r) (s) (t)

Figure 6.10: (Color online) Minimum energy configurations for C ≥ 1/2, ρ = 0.6, and z = 0.3296.
107
6.4 Conclusions 108

along the direction of the magnetic field, the particles form chains aligned parallel to
the field. By varying the degree of anisotropy and density we found a rich spectrum
of new structures.
Chapter 7

Conclusions

This thesis is divided into three parts. The first part contains two studies of ph-
ysisorbed polymers (linear and star) on surfaces. In the second part, an attempt has
been made to realise a scale-free near-neighbour network in computer simulations
of polydisperse fluids of hard disks. In the final part we explore the minimum en-
ergy configurations of two dimensional binary mixture of magnetic colloids in tilted
external fields.
In the first part, we were motivated by atomic-force microscopy images of poly-
mer films (either linear chains or stars), on mica surfaces, adsorbed from dilute
solution following a good solvent-to-bad solvent quenching transition. In the case
of linear chains a bimodal cluster distribution is observed under certain experimen-
tal conditions. We used a bead-spring molecular model and Langevin dynamics
computer simulations and demonstrated that a bimodal distribution can be repro-
duced in the simulations and rationalised on the basis of the polymer structures
prior to the quench. In addition to providing insight on experimental observations,
the simulation results support a number of predicted scaling laws such as the decay
of the monomer density as a function of distance from the surface. Additionally,
the same methodology has been used to study many arms stars polymers, in which
the soft-colloidal nature of star polymers was studied in the proximity of a surface.
Measurements of the fraction of monomers bound to the surface, height, radius
of gyration and asphericity provided valuable insights on the structures. We ratio-
nalised the results and allowed us to map the stars’ behaviours (from polymer-like to
soft-colloid) based on the number of arms and their length on a given surface.
In the second part of this thesis we examine the neighbour network in a two-
dimensional polydisperse hard-disk fluid with diameter distribution p(σ) ∼ σ−4 is
examined using constant-pressure Monte Carlo simulations.Graphs are constructed
from vertices (disks) with edges (links) connecting each vertex to k neighbouring

109
7 Conclusions 110

vertices defined by radical tessellation. At packing fractions in the range 0.24 ≤ η ≤


0.36, the decay of the network degree distribution is observed to be consistent with
the power-law k −γ where the exponent lies in the range 5.6 ≤ γ ≤ 6.0. Comparisons
with the predictions of a maximum-entropy theory suggest that this apparent power-
law behaviour is not the asymptotic one, and that p k ∼ k −4 in the limit k → ∞. This
asymptotic dependence is consistent with the simple idea that for large disks, the
number of neighbours is proportional to the disk diameter. A power-law decay of
the network degree distribution is one of the characteristics of a scale-free network.
The assortativity of the network is measured, and is found to be positive, meaning
that vertices of equal degree are connected more often than in a random network.
Finally, the equation of state is determined and compared with the prediction from
a scaled-particle theory. Very good agreement between simulation and theory is
demonstrated.
In the final part, we use genetic algorithms, which allow to efficiently search
energy landscapes and obtain their global minimum, to investigate the ordered
equilibrium structures formed by binary mixtures of anisotropic dipolar particles
confined to a plane, under the presence of an external magnetic field. Anisotropy
is introduced by tilting the external magnetic field with respect to the interface.
Initially, as the field is tilted the isotropic structures are perturbed only slightly, but
as anisotropy becomes enhanced by tilting the magnetic field further new structures
emerge. Once anisotropy becomes dominant, the structures form chains parallel to
the field.
Appendix A

Appendix - Papers published

1. Magnetic properties of polydisperse ferrofluids: A critical comparison between


experiment, theory and computer simulation, A. O. Ivanov, S. S. Kantorovich,
E. N. Reznikov, C. Holm, A. F. Pshenichnikov, A. V. Lebedev, A. Chremos, and P. J.
Camp, Phys. Rev. E 75, 061405 (2007).

2. Polymer-like to soft colloid-like behavior of regular star polymers adsorbed


on surfaces, E. Glynos, A. Chremos, G. Petekidis, P. J. Camp, and V. Koutsos,
Macromolecules 40, 6947-6958 (2007).

3. Neighbor network in a polydisperse hard-disk fluid: degree distribution and


assortativity, A. Chremos and P. J. Camp, Phys. Rev. E 76, 056108 (2007).

4. Magnetic measurements as a key for the particle size distribution in ferrofluids:


experiment, theory, and computer simulations, A. O. Ivanov, S. S. Kantorovich,
E. N. Reznikov, C. Holm, A. F. Pshenichnikov, A. V. Lebedev, A. Chremos, and P. J.
Camp, Magnetohydrodynamics 43, 393-400 (2007).

5. Adsorption and self-assembly of linear polymers on surfaces: A computer sim-


ulation study, A. Chremos, E. Glynos, V. Koutsos, and P. J. Camp, Soft Matter,
accepted (2008).

6. Collapsing and clustering after solvent evaporation of physisorbed linear ho-


mopolymer on surfaces: an atomic force microscopy study, E. Glynos, A. Chre-
mos, P. J. Camp, E. Theofanidou, and V. Koutsos, submitted to Macromolecules.

7. Adsorption and self-assembly of star polymers on surfaces: A computer simula-


tion study, A. Chremos, E. Glynos, V. Koutsos and P. J. Camp, in preparation.

8. Crystal structures of two-dimensional binary mixtures of dipolar colloids in


tilted external fields, A. Chremos and C. N. Likos, in preparation.

111
A Appendix - Papers published 112

9. Complex fluid and solid structures of binary core-softened particles, A. C. Fogarty,


A. Chremos, and P. J. Camp, in preparation.
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